Molecular oxygen

evidence_span

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experimental_model

Review of prolyl 4-hydroxylase enzymology and subunit structure

exposure

Hydroxylation of proline in X-Pro-Gly sequences

limitations

An authoritative enzymology review rather than a single experiment. It is the source for the cosubstrate list, which is the point at which oxygen, iron and vitamin C meet in collagen synthesis.

nutrient_topic

Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Hyperbaric oxygen therapy

organism

Mammalian enzyme

plain_language

Making collagen needs oxygen, iron, vitamin C and a Krebs-cycle acid, all four at once.

primary_references

[hbot-p2537773] Protein hydroxylation: prolyl 4-hydroxylase, an enzyme with four cosubstrates and a multifunctional subunit. (1989). https://pubmed.ncbi.nlm.nih.gov/2537773/ DOI: 10.1096/fasebj.3.5.2537773

tissue_or_cell_type

Endoplasmic reticulum

Hyperbaric oxygen: the exposure, its reactive species, the signals they carry, and the nutrient-dependent enzymes that handle them (2026-09-19) · lines 855–866

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Review of prolyl 4-hydroxylase enzymology and subunit structure · source_derived_draft · unverified_draft

### hbot-p4h-cosubstrates Prolyl 4-hydroxylase catalyses formation of 4-hydroxyproline in collagens by hydroxylating proline residues in X-Pro-Gly sequences, and the reaction requires Fe2+, 2-oxoglutarate, O2 and ascorbate, involving oxidative decarboxylation of 2-oxoglutarate. Condition category: normal nutrient_topic: Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: Making collagen needs oxygen, iron, vitamin C and a Krebs-cycle acid, all four at once. organism: Mammalian enzyme tissue_or_cell_type: Endoplasmic reticulum experimental_model: Review of prolyl 4-hydroxylase enzymology and subunit structure limitations: An authoritative enzymology review rather than a single experiment. It is the source for the cosubstrate list, which is the point at which oxygen, iron and vitamin C meet in collagen synthesis. exposure: Hydroxylation of proline in X-Pro-Gly sequences evidence_span: {"source_cache": "artifacts/hbot-research/2537773.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "3fdda2e4cf4392ec7a88b137274cee8f321255473992a2d8df781df12cad6cfe", "start_char": 0, "end_char": 2024, "text_sha256": "3fdda2e4cf4392ec7a88b137274cee8f321255473992a2d8df781df12cad6cfe"} [hbot-p2537773] Protein hydroxylation: prolyl 4-hydroxylase, an enzyme with four cosubstrates and a multifunctional subunit. (1989). https://pubmed.ncbi.nlm.nih.gov/2537773/ DOI: 10.1096/fasebj.3.5.2537773

evidence_access

Primary abstract

experimental_model

Human enzyme; 1.7-angstrom structures and spectroscopy.

limitations

DOHH is not a collagen-type 2-oxoglutarate hydroxylase; do not infer the same vitamin C requirement.

nutrient_topic

Spermidine collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Spermidine

plain_language

Oxygen chemistry completes the protein modification.

primary_references

Crystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination. · 2015 · https://pubmed.ncbi.nlm.nih.gov/25865244/ · DOI 10.1016/j.str.2015.03.002

Spermidine: biosynthesis, hypusination, transport and cross-nutrient mechanisms (2026-09-19) · lines 62–68

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Human enzyme; 1.7-angstrom structures and spectroscopy. · source_derived_draft · unverified_draft

## spermidine-dohh-oxygen Oxygen chemistry completes the protein modification. Human DOHH structures resolved a peroxo-diiron intermediate involved in hydroxylating deoxyhypusine-eIF5A. Model: Human enzyme; 1.7-angstrom structures and spectroscopy. Limitations: DOHH is not a collagen-type 2-oxoglutarate hydroxylase; do not infer the same vitamin C requirement. Evidence access: Primary abstract Crystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination. · 2015 · https://pubmed.ncbi.nlm.nih.gov/25865244/ · DOI 10.1016/j.str.2015.03.002

evidence_span

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experimental_model

Recombinant human MOCS1A, cysteine mutagenesis and multiple spectroscopic methods

exposure

Aerobic versus anaerobic purification; iron-sulfur reconstitution

limitations

Purified protein exposure; not evidence that normal breathing causes cofactor deficiency.

nutrient_topic

Molybdenum research collection; topical membership is not evidence of a direct dietary effect. · Molybdenum

organism

Human protein expressed in Escherichia coli

plain_language

The assembly protein contains oxygen-sensitive clusters.

primary_references

[mo-p15180982] Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis. (2004). https://pubmed.ncbi.nlm.nih.gov/15180982/ DOI: 10.1074/jbc.m313398200

tissue_or_cell_type

Purified protein and bacterial complementation

Molybdenum: cofactor assembly, sulfur metabolism and nutrient interactions (2026-09-17) · lines 339–350

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human MOCS1A, cysteine mutagenesis and multiple spectroscopic methods · source_derived_draft · unverified_draft

### mo-mocs1a-oxygen Oxygen rapidly degraded both reconstituted MOCS1A [4Fe-4S] clusters, producing different semistable cluster intermediates. Condition category: normal nutrient_topic: Molybdenum research collection; topical membership is not evidence of a direct dietary effect. plain_language: The assembly protein contains oxygen-sensitive clusters. organism: Human protein expressed in Escherichia coli tissue_or_cell_type: Purified protein and bacterial complementation experimental_model: Recombinant human MOCS1A, cysteine mutagenesis and multiple spectroscopic methods limitations: Purified protein exposure; not evidence that normal breathing causes cofactor deficiency. exposure: Aerobic versus anaerobic purification; iron-sulfur reconstitution evidence_span: {"source_cache": "artifacts/molybdenum-research/15180982.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "722c11f1c29a720fb7105f37962af2652ce95b6734afdb59d675dee0b8302097", "start_char": 0, "end_char": 1828, "text_sha256": "722c11f1c29a720fb7105f37962af2652ce95b6734afdb59d675dee0b8302097"} [mo-p15180982] Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis. (2004). https://pubmed.ncbi.nlm.nih.gov/15180982/ DOI: 10.1074/jbc.m313398200

evidence_location

Abstract

experimental_model

Recombinant human BCO1 with isotopically labeled oxygen and water.

exposure

18O2 versus H2-18O incubations with beta-carotene.

limitations

Reaction chemistry; no claim about clinical hypoxia or oxygen supplementation.

nutrient_topic

Vitamin A research collection; topical membership is not evidence of a direct dietary effect. · Vitamin A

organism

Homo sapiens recombinant protein

outcome

Isotope tracing showed that oxygen incorporated into both BCO1-generated retinal products originated from molecular oxygen.

plain_language

BCO1 cleavage uses oxygen gas to make the two retinal aldehydes.

primary_references

[va-delasena-2014] The human enzyme that converts dietary provitamin A carotenoids to vitamin A is a dioxygenase (2014). https://pubmed.ncbi.nlm.nih.gov/24668807/ DOI: 10.1074/jbc.M114.557710

tissue_or_cell_type

Cell-free enzyme

Vitamin A: forms, mechanisms, deficiency and excess (2026-09-17) · lines 173–185

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human BCO1 with isotopically labeled oxygen and water. · source_derived_draft · unverified_draft

### va-bco1-dioxygen-incorporation Isotope tracing showed that oxygen incorporated into both BCO1-generated retinal products originated from molecular oxygen. Condition category: normal nutrient_topic: Vitamin A research collection; topical membership is not evidence of a direct dietary effect. plain_language: BCO1 cleavage uses oxygen gas to make the two retinal aldehydes. organism: Homo sapiens recombinant protein tissue_or_cell_type: Cell-free enzyme experimental_model: Recombinant human BCO1 with isotopically labeled oxygen and water. limitations: Reaction chemistry; no claim about clinical hypoxia or oxygen supplementation. exposure: 18O2 versus H2-18O incubations with beta-carotene. outcome: Isotope tracing showed that oxygen incorporated into both BCO1-generated retinal products originated from molecular oxygen. evidence_location: Abstract [va-delasena-2014] The human enzyme that converts dietary provitamin A carotenoids to vitamin A is a dioxygenase (2014). https://pubmed.ncbi.nlm.nih.gov/24668807/ DOI: 10.1074/jbc.M114.557710

evidence_span

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experimental_model

Purified reconstructed COQ metabolon with short-chain substrates

exposure

Enzyme combinations, methyl donors, reductants and metal additions

limitations

Ancestral proteins and CoQ1 analogues; no clinical cofactor dose or proof of nutritional rate limitation. Reaction order need not be universal across species.

nutrient_topic

Coenzyme Q10 research collection; topical membership is not evidence of a direct dietary effect. · Coenzyme Q10 / CoQ10 redox system

organism

Reconstructed ancestral tetrapod proteins

plain_language

The monooxygenase needed its electron-supplying partners.

primary_references

[coq10-p38425362] In vitro construction of the COQ metabolon unveils the molecular determinants of coenzyme Q biosynthesis. (2024). https://pubmed.ncbi.nlm.nih.gov/38425362/ DOI: 10.1038/s41929-023-01087-z

tissue_or_cell_type

Stepwise CoQ head-group assembly

Coenzyme Q10: biosynthesis, electron transfer, antioxidant recycling and nutrient interactions (2026-09-17) · lines 632–643

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified reconstructed COQ metabolon with short-chain substrates · source_derived_draft · unverified_draft

### coq10-fdx2-coq6 COQ6 substrate conversion required the FDXR-FDX2 pair in the reconstructed assay. Condition category: normal nutrient_topic: Coenzyme Q10 research collection; topical membership is not evidence of a direct dietary effect. plain_language: The monooxygenase needed its electron-supplying partners. organism: Reconstructed ancestral tetrapod proteins tissue_or_cell_type: Stepwise CoQ head-group assembly experimental_model: Purified reconstructed COQ metabolon with short-chain substrates limitations: Ancestral proteins and CoQ1 analogues; no clinical cofactor dose or proof of nutritional rate limitation. Reaction order need not be universal across species. exposure: Enzyme combinations, methyl donors, reductants and metal additions evidence_span: {"source_cache": "artifacts/coq10-research/38425362.fulltext.txt", "locator": "Primary full-text span; zero-based, end-exclusive Unicode character offsets", "file_sha256": "7d25af4ecd7340649536b8fea3b8a0a308a1611bbf8c57f6a79b362f443f1cba", "start_char": 9067, "end_char": 13813, "text_sha256": "49612ae4d3a59a75a02fe3fb132abd8aeb7ef8b7cae3b0f79b5557503c55ad51"} [coq10-p38425362] In vitro construction of the COQ metabolon unveils the molecular determinants of coenzyme Q biosynthesis. (2024). https://pubmed.ncbi.nlm.nih.gov/38425362/ DOI: 10.1038/s41929-023-01087-z

evidence_span

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experimental_model

Oxygen-isotope metabolomics and enzyme perturbation

exposure

18O2 labeling and HPDL activity

limitations

Cellular pathway; no evidence that additional tyrosine treats every CoQ deficiency.

nutrient_topic

Coenzyme Q10 research collection; topical membership is not evidence of a direct dietary effect. · Coenzyme Q10 / CoQ10 redox system

organism

Human cell lines

plain_language

A separate enzyme helps make the head of the CoQ molecule.

primary_references

[coq10-p34471290] The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway. (2021). https://pubmed.ncbi.nlm.nih.gov/34471290/ DOI: 10.1038/s41586-021-03865-w

tissue_or_cell_type

Tyrosine-derived CoQ head-group precursor

Coenzyme Q10: biosynthesis, electron transfer, antioxidant recycling and nutrient interactions (2026-09-17) · lines 164–175

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Oxygen-isotope metabolomics and enzyme perturbation · source_derived_draft · unverified_draft

### coq10-hpdl-hma HPDL produced 4-hydroxymandelate in human cells. Condition category: normal nutrient_topic: Coenzyme Q10 research collection; topical membership is not evidence of a direct dietary effect. plain_language: A separate enzyme helps make the head of the CoQ molecule. organism: Human cell lines tissue_or_cell_type: Tyrosine-derived CoQ head-group precursor experimental_model: Oxygen-isotope metabolomics and enzyme perturbation limitations: Cellular pathway; no evidence that additional tyrosine treats every CoQ deficiency. exposure: 18O2 labeling and HPDL activity evidence_span: {"source_cache": "artifacts/coq10-research/34471290.abstract.txt", "locator": "Primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "a3cbcc69203ace49d0451e55c2d4040109e16facb575f4d66a0396d375ba8956", "start_char": 0, "end_char": 1028, "text_sha256": "a3cbcc69203ace49d0451e55c2d4040109e16facb575f4d66a0396d375ba8956"} [coq10-p34471290] The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway. (2021). https://pubmed.ncbi.nlm.nih.gov/34471290/ DOI: 10.1038/s41586-021-03865-w

evidence_span

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experimental_model

Review of prolyl 4-hydroxylase enzymology and subunit structure

exposure

Hydroxylation of proline in X-Pro-Gly sequences

limitations

An authoritative enzymology review rather than a single experiment. It is the source for the cosubstrate list, which is the point at which oxygen, iron and vitamin C meet in collagen synthesis.

nutrient_topic

Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Hyperbaric oxygen therapy

organism

Mammalian enzyme

plain_language

Vitamin C is not used up every turn; it is the reserve that resets the enzyme when a cycle misfires.

primary_references

[hbot-p2537773] Protein hydroxylation: prolyl 4-hydroxylase, an enzyme with four cosubstrates and a multifunctional subunit. (1989). https://pubmed.ncbi.nlm.nih.gov/2537773/ DOI: 10.1096/fasebj.3.5.2537773

tissue_or_cell_type

Endoplasmic reticulum

Hyperbaric oxygen: the exposure, its reactive species, the signals they carry, and the nutrient-dependent enzymes that handle them (2026-09-19) · lines 868–879

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Review of prolyl 4-hydroxylase enzymology and subunit structure · source_derived_draft · unverified_draft

### hbot-ascorbate-uncoupled-cycles Ascorbate is not consumed during most catalytic cycles, but the enzyme also decarboxylates 2-oxoglutarate without subsequent hydroxylation, and ascorbate is required as a specific alternative oxygen acceptor in those uncoupled cycles. Condition category: normal nutrient_topic: Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: Vitamin C is not used up every turn; it is the reserve that resets the enzyme when a cycle misfires. organism: Mammalian enzyme tissue_or_cell_type: Endoplasmic reticulum experimental_model: Review of prolyl 4-hydroxylase enzymology and subunit structure limitations: An authoritative enzymology review rather than a single experiment. It is the source for the cosubstrate list, which is the point at which oxygen, iron and vitamin C meet in collagen synthesis. exposure: Hydroxylation of proline in X-Pro-Gly sequences evidence_span: {"source_cache": "artifacts/hbot-research/2537773.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "3fdda2e4cf4392ec7a88b137274cee8f321255473992a2d8df781df12cad6cfe", "start_char": 0, "end_char": 2024, "text_sha256": "3fdda2e4cf4392ec7a88b137274cee8f321255473992a2d8df781df12cad6cfe"} [hbot-p2537773] Protein hydroxylation: prolyl 4-hydroxylase, an enzyme with four cosubstrates and a multifunctional subunit. (1989). https://pubmed.ncbi.nlm.nih.gov/2537773/ DOI: 10.1096/fasebj.3.5.2537773

evidence_span

{"source_cache": "artifacts/hbot-research/17003127.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "8c7def7926cf3f7a38d874fe22494fa3b72477ed41bdd2baee407cab4ea0d96d", "start_char": 0, "end_char": 1302, "text_sha256": "8c7def7926cf3f7a38d874fe22494fa3b72477ed41bdd2baee407cab4ea0d96d"}

experimental_model

Stopped-flow, optical absorption and Mossbauer spectroscopy of a prolyl-4-hydroxylase reaction

exposure

Catalysis with saturating substrates and deuterated substrate

limitations

Spectroscopy on a functional homologue, not the human enzyme. It identifies the chemical intermediate that does the work.

nutrient_topic

Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Hyperbaric oxygen therapy

organism

Bacterial enzyme homologous to the human enzymes

plain_language

The iron atom briefly becomes a highly reactive form that rips a hydrogen off the target carbon.

primary_references

[hbot-p17003127] Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase. (2006). https://pubmed.ncbi.nlm.nih.gov/17003127/ DOI: 10.1073/pnas.0604005103

tissue_or_cell_type

Purified enzyme

Hyperbaric oxygen: the exposure, its reactive species, the signals they carry, and the nutrient-dependent enzymes that handle them (2026-09-19) · lines 894–905

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Stopped-flow, optical absorption and Mossbauer spectroscopy of a prolyl-4-hydroxylase reaction · source_derived_draft · unverified_draft

### hbot-fe-iv-intermediate A prolyl-4-hydroxylase, a functional homologue of human 2-oxoglutarate-dependent dioxygenases with essential roles in collagen biosynthesis and oxygen sensing, accumulated a C-H-cleaving high-spin Fe(IV)-oxo intermediate with a large substrate deuterium kinetic isotope effect on its decay. Condition category: normal nutrient_topic: Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: The iron atom briefly becomes a highly reactive form that rips a hydrogen off the target carbon. organism: Bacterial enzyme homologous to the human enzymes tissue_or_cell_type: Purified enzyme experimental_model: Stopped-flow, optical absorption and Mossbauer spectroscopy of a prolyl-4-hydroxylase reaction limitations: Spectroscopy on a functional homologue, not the human enzyme. It identifies the chemical intermediate that does the work. exposure: Catalysis with saturating substrates and deuterated substrate evidence_span: {"source_cache": "artifacts/hbot-research/17003127.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "8c7def7926cf3f7a38d874fe22494fa3b72477ed41bdd2baee407cab4ea0d96d", "start_char": 0, "end_char": 1302, "text_sha256": "8c7def7926cf3f7a38d874fe22494fa3b72477ed41bdd2baee407cab4ea0d96d"} [hbot-p17003127] Direct spectroscopic detection of a C-H-cleaving high-spin Fe(IV) complex in a prolyl-4-hydroxylase. (2006). https://pubmed.ncbi.nlm.nih.gov/17003127/ DOI: 10.1073/pnas.0604005103

evidence_span

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experimental_model

Narrative review of therapeutic mechanisms and clinical trial evidence

exposure

Hyperbaric oxygen as used clinically, typically 2.0 to 2.5 atmospheres absolute

limitations

A narrative review, not a primary experiment. It is recorded as the framing source the reader was given; every mechanism it names is also recorded here from its own primary paper.

nutrient_topic

Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Hyperbaric oxygen therapy

organism

Human, with supporting animal work

plain_language

The therapy works by making the cell produce reactive molecules that carry signals, not simply by supplying more oxygen.

primary_references

[hbot-p21200283] Hyperbaric oxygen: its mechanisms and efficacy. (2011). https://pubmed.ncbi.nlm.nih.gov/21200283/ DOI: 10.1097/prs.0b013e3181fbe2bf

tissue_or_cell_type

Multiple tissues

Hyperbaric oxygen: the exposure, its reactive species, the signals they carry, and the nutrient-dependent enzymes that handle them (2026-09-19) · lines 62–73

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Narrative review of therapeutic mechanisms and clinical trial evidence · source_derived_draft · unverified_draft

### hbot-review-reactive-species-framing The review states that the principal mechanisms of hyperbaric oxygen are based on intracellular generation of reactive species of oxygen and nitrogen, which act through cell signal transduction cascades. Condition category: normal nutrient_topic: Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: The therapy works by making the cell produce reactive molecules that carry signals, not simply by supplying more oxygen. organism: Human, with supporting animal work tissue_or_cell_type: Multiple tissues experimental_model: Narrative review of therapeutic mechanisms and clinical trial evidence limitations: A narrative review, not a primary experiment. It is recorded as the framing source the reader was given; every mechanism it names is also recorded here from its own primary paper. exposure: Hyperbaric oxygen as used clinically, typically 2.0 to 2.5 atmospheres absolute evidence_span: {"source_cache": "artifacts/hbot-research/21200283.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "541f2eb700a843e35093e589069b7839f1a3577c2de8cd1edb444698c1379380", "start_char": 0, "end_char": 1120, "text_sha256": "541f2eb700a843e35093e589069b7839f1a3577c2de8cd1edb444698c1379380"} [hbot-p21200283] Hyperbaric oxygen: its mechanisms and efficacy. (2011). https://pubmed.ncbi.nlm.nih.gov/21200283/ DOI: 10.1097/prs.0b013e3181fbe2bf

evidence_span

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experimental_model

Refinement of the 2 angstrom crystal structure of copper, zinc superoxide dismutase with molecular surface analysis

exposure

Structural and mechanistic analysis of the active site

limitations

Structural chemistry. It explains why the enzyme needs its metals; it is not a statement about dietary copper or zinc.

nutrient_topic

Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Hyperbaric oxygen therapy

organism

Bovine enzyme structure

plain_language

The copper atom itself is what takes and gives back the electron.

primary_references

[hbot-p6316150] Structure and mechanism of copper, zinc superoxide dismutase. (1983). https://pubmed.ncbi.nlm.nih.gov/6316150/ DOI: 10.1038/306284a0

tissue_or_cell_type

Purified enzyme

Hyperbaric oxygen: the exposure, its reactive species, the signals they carry, and the nutrient-dependent enzymes that handle them (2026-09-19) · lines 491–502

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Refinement of the 2 angstrom crystal structure of copper, zinc superoxide dismutase with molecular surface analysis · source_derived_draft · unverified_draft

### hbot-sod1-copper-mechanism Copper, zinc superoxide dismutase catalyses the two-step dismutation of superoxide to molecular oxygen and hydrogen peroxide through alternate reduction and oxidation of the active-site copper, with a single complementary binding position for superoxide at the Cu(II) and the activity-important Arg141. Condition category: normal nutrient_topic: Hyperbaric oxygen research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: The copper atom itself is what takes and gives back the electron. organism: Bovine enzyme structure tissue_or_cell_type: Purified enzyme experimental_model: Refinement of the 2 angstrom crystal structure of copper, zinc superoxide dismutase with molecular surface analysis limitations: Structural chemistry. It explains why the enzyme needs its metals; it is not a statement about dietary copper or zinc. exposure: Structural and mechanistic analysis of the active site evidence_span: {"source_cache": "artifacts/hbot-research/6316150.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "dc20323f9774c6c743e01f8bdbeedbc42b0ddac982f1e17d53a9591b87bf5379", "start_char": 0, "end_char": 867, "text_sha256": "dc20323f9774c6c743e01f8bdbeedbc42b0ddac982f1e17d53a9591b87bf5379"} [hbot-p6316150] Structure and mechanism of copper, zinc superoxide dismutase. (1983). https://pubmed.ncbi.nlm.nih.gov/6316150/ DOI: 10.1038/306284a0

evidence_access

Primary abstract

experimental_model

Human apo and iron-bound HGD crystallography.

limitations

The study is structural/enzymatic evidence, not a trial of iron supplementation.

nutrient_topic

L-Tyrosine collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Tyrosine

plain_language

Iron-dependent chemistry opens the aromatic ring for further breakdown.

primary_references

Crystal structure of human homogentisate dioxygenase. · 2000 · https://pubmed.ncbi.nlm.nih.gov/10876237/ · DOI 10.1038/76756

L-Tyrosine: catecholamines, thyroid chemistry, pigment, metabolism and cross-nutrient mechanisms (2026-09-19) · lines 236–242

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Human apo and iron-bound HGD crystallography. · source_derived_draft · unverified_draft

## l-tyrosine-hgd-ring Iron-dependent chemistry opens the aromatic ring for further breakdown. Human HGD catalyzes aromatic-ring cleavage during phenylalanine/tyrosine degradation; its structure contains a coordinated active-site iron ion. Model: Human apo and iron-bound HGD crystallography. Limitations: The study is structural/enzymatic evidence, not a trial of iron supplementation. Evidence access: Primary abstract Crystal structure of human homogentisate dioxygenase. · 2000 · https://pubmed.ncbi.nlm.nih.gov/10876237/ · DOI 10.1038/76756

evidence_access

Primary abstract

experimental_model

Human enzyme mutagenesis, binding assays and structural simulation.

limitations

HPD must not be merged with HPDL, which has a different product.

nutrient_topic

L-Tyrosine collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Tyrosine

plain_language

The carbon skeleton passes through a separate oxygen-dependent enzyme.

primary_references

Functional role of residues involved in substrate binding of human 4-hydroxyphenylpyruvate dioxygenase. · 2021 · https://pubmed.ncbi.nlm.nih.gov/34047349/ · DOI 10.1042/BCJ20210005

L-Tyrosine: catecholamines, thyroid chemistry, pigment, metabolism and cross-nutrient mechanisms (2026-09-19) · lines 228–234

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Human enzyme mutagenesis, binding assays and structural simulation. · source_derived_draft · unverified_draft

## l-tyrosine-hpd-hga The carbon skeleton passes through a separate oxygen-dependent enzyme. Human HPD converts 4-hydroxyphenylpyruvate to homogentisate; substrate-binding-site mutations altered catalytic efficiency. Model: Human enzyme mutagenesis, binding assays and structural simulation. Limitations: HPD must not be merged with HPDL, which has a different product. Evidence access: Primary abstract Functional role of residues involved in substrate binding of human 4-hydroxyphenylpyruvate dioxygenase. · 2021 · https://pubmed.ncbi.nlm.nih.gov/34047349/ · DOI 10.1042/BCJ20210005

evidence_access

Primary full text; Results and catalytic assays

experimental_model

Human intramelanosomal domain expressed in insect cells; activity assays.

limitations

Same metabolite identity as L-DOPA in catecholamine synthesis, but different enzyme and compartment.

nutrient_topic

L-Tyrosine collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Tyrosine

plain_language

A different enzyme uses the same amino acid for pigment chemistry.

primary_references

Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity. · 2014 · https://pubmed.ncbi.nlm.nih.gov/24392141/ · DOI 10.1371/journal.pone.0084494

L-Tyrosine: catecholamines, thyroid chemistry, pigment, metabolism and cross-nutrient mechanisms (2026-09-19) · lines 148–154

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Human intramelanosomal domain expressed in insect cells; activity assays. · source_derived_draft · unverified_draft

## l-tyrosine-tyr-dopa A different enzyme uses the same amino acid for pigment chemistry. Purified recombinant human tyrosinase showed monophenolase activity with L-tyrosine, the initial hydroxylation step toward pigment. Model: Human intramelanosomal domain expressed in insect cells; activity assays. Limitations: Same metabolite identity as L-DOPA in catecholamine synthesis, but different enzyme and compartment. Evidence access: Primary full text; Results and catalytic assays Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity. · 2014 · https://pubmed.ncbi.nlm.nih.gov/24392141/ · DOI 10.1371/journal.pone.0084494

evidence_access

Primary full text; Results and catalytic assays

experimental_model

Purified human enzyme; L-DOPA colorimetric assays.

limitations

A colorimetric enzyme rate does not establish whole-body melanin output.

nutrient_topic

L-Tyrosine collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Tyrosine

plain_language

The pigment route includes a separate oxidation step.

primary_references

Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity. · 2014 · https://pubmed.ncbi.nlm.nih.gov/24392141/ · DOI 10.1371/journal.pone.0084494

L-Tyrosine: catecholamines, thyroid chemistry, pigment, metabolism and cross-nutrient mechanisms (2026-09-19) · lines 156–162

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Purified human enzyme; L-DOPA colorimetric assays. · source_derived_draft · unverified_draft

## l-tyrosine-tyr-quinone The pigment route includes a separate oxidation step. Recombinant human tyrosinase also showed diphenol oxidase activity with L-DOPA, supporting the next oxidation toward dopaquinone. Model: Purified human enzyme; L-DOPA colorimetric assays. Limitations: A colorimetric enzyme rate does not establish whole-body melanin output. Evidence access: Primary full text; Results and catalytic assays Albinism-causing mutations in recombinant human tyrosinase alter intrinsic enzymatic activity. · 2014 · https://pubmed.ncbi.nlm.nih.gov/24392141/ · DOI 10.1371/journal.pone.0084494

dose

Tartrazine/isolated metabolites; preparative concentrations not recovered from primary abstract

duration

Reaction intervals not recovered from accessed abstract

evidence_access

Primary PubMed abstract; unrecovered method details explicitly retained.

evidence_scope

literature_reviewed; source-specific experimental curation

experimental_model

Human-stool bacterial isolates and analytical chemistry of tartrazine products

limitations

SCAP and PPA identities were experimentally characterized. The additional yellow derivative remains proposed and is not imported as an established metabolite. Human circulating exposure was not measured.

nutrient_topic

Tartrazine food-colorant chapter; nutrient, drug and peptide interactions retain their models and limits. · Tartrazine

organism

Human-stool bacterial isolates and analytical chemistry of tartrazine products

plain_language

SCAP oxidation on exposure to air produced the characterized purple derivative purpurazoic acid.

primary_references

Preparation, analysis and toxicity characterisation of the redox metabolites of the azo food dye tartrazine. (2023). https://pubmed.ncbi.nlm.nih.gov/37980979/ DOI: 10.1016/j.fct.2023.114193

route

In vitro biotransformation and chemical characterization

tissue

Azo reduction followed by oxidation on exposure to air

Tartrazine: mechanisms, molecular forms and cross-actor connections (2026-09-20) · lines 105–114

Original AI-assisted curation of eighteen primary studies. Study-specific citations, negative findings and limitations retained. Not publisher full text. · supports · Human-stool bacterial isolates and analytical chemistry of tartrazine products · source_derived_draft · unverified_draft

## tartrazine-ppa-oxidation SCAP oxidation on exposure to air produced the characterized purple derivative purpurazoic acid. Model/species: Human-stool bacterial isolates and analytical chemistry of tartrazine products Tissue: Azo reduction followed by oxidation on exposure to air Exposure: Tartrazine/isolated metabolites; preparative concentrations not recovered from primary abstract Route: In vitro biotransformation and chemical characterization Duration: Reaction intervals not recovered from accessed abstract Limits: SCAP and PPA identities were experimentally characterized. The additional yellow derivative remains proposed and is not imported as an established metabolite. Human circulating exposure was not measured. Primary reference: Preparation, analysis and toxicity characterisation of the redox metabolites of the azo food dye tartrazine. (2023). https://pubmed.ncbi.nlm.nih.gov/37980979/ DOI: 10.1016/j.fct.2023.114193 Access: Primary PubMed abstract; unrecovered method details explicitly retained.

evidence_access

Primary abstract

experimental_model

Purified recombinant human DOHH; EPR, Mossbauer, XAS and Raman spectroscopy.

limitations

Not a clinical iron-deficiency threshold or evidence that extra iron improves spermidine responses.

nutrient_topic

Spermidine collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Spermidine

plain_language

Iron is part of the enzyme that completes hypusination.

primary_references

Human deoxyhypusine hydroxylase, an enzyme involved in regulating cell growth, activates O2 with a nonheme diiron center. · 2009 · https://pubmed.ncbi.nlm.nih.gov/19706422/ · DOI 10.1073/pnas.0904553106

Spermidine: biosynthesis, hypusination, transport and cross-nutrient mechanisms (2026-09-19) · lines 54–60

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Purified recombinant human DOHH; EPR, Mossbauer, XAS and Raman spectroscopy. · source_derived_draft · unverified_draft

## spermidine-dohh-iron Iron is part of the enzyme that completes hypusination. Spectroscopy established a coupled diiron center in human DOHH, whose reduced state activates oxygen. Model: Purified recombinant human DOHH; EPR, Mossbauer, XAS and Raman spectroscopy. Limitations: Not a clinical iron-deficiency threshold or evidence that extra iron improves spermidine responses. Evidence access: Primary abstract Human deoxyhypusine hydroxylase, an enzyme involved in regulating cell growth, activates O2 with a nonheme diiron center. · 2009 · https://pubmed.ncbi.nlm.nih.gov/19706422/ · DOI 10.1073/pnas.0904553106

evidence_access

Primary abstract

experimental_model

Purified porcine enzyme oxidative half-reaction.

limitations

This chemistry alone does not demonstrate oxidative injury after human oral supplementation.

nutrient_topic

D-Aspartate collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · D-Aspartate

plain_language

Clearing D-aspartate also generates a peroxide-handling requirement.

primary_references

Functional and structural characterization of D-aspartate oxidase from porcine kidney: non-Michaelis kinetics due to substrate activation. · 2007 · https://pubmed.ncbi.nlm.nih.gov/17234685/ · DOI 10.1093/jb/mvm041

D-Aspartate: synthesis, clearance, neural and endocrine mechanisms (2026-09-19) · lines 112–118

AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Purified porcine enzyme oxidative half-reaction. · source_derived_draft · unverified_draft

## d-aspartate-ddo-peroxide Clearing D-aspartate also generates a peroxide-handling requirement. Reoxidation of reduced FAD by oxygen during porcine DDO turnover produced hydrogen peroxide. Model: Purified porcine enzyme oxidative half-reaction. Limitations: This chemistry alone does not demonstrate oxidative injury after human oral supplementation. Evidence access: Primary abstract Functional and structural characterization of D-aspartate oxidase from porcine kidney: non-Michaelis kinetics due to substrate activation. · 2007 · https://pubmed.ncbi.nlm.nih.gov/17234685/ · DOI 10.1093/jb/mvm041

cross_nutrient

Heme iron participates in a tryptophan-to-niacin upstream enzyme; the structure does not establish a dietary iron threshold.

evidence_span

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experimental_model

Purified human TDO2 crystallography and spectroscopy; substrate/product complexes

exposure

Biochemical or structural assay; no dietary intervention

limitations

Purified-enzyme evidence does not establish dietary intake requirements or clinical outcomes.

nutrient_topic

Niacin research collection; topical membership is not evidence of a direct dietary effect. · Niacin (vitamin B3)

organism

Homo sapiens

plain_language

Iron held in heme positions oxygen for this precursor reaction.

primary_references

[b3-pre-tdo2016] Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase. (2016). https://pubmed.ncbi.nlm.nih.gov/27762317/ DOI: 10.1038/srep35169

tissue_or_cell_type

Purified recombinant protein; no intact tissue

Niacin: NAD metabolism, deficiency and nutrient interactions (2026-09-17) · lines 493–505

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human TDO2 crystallography and spectroscopy; substrate/product complexes · source_derived_draft · unverified_draft

### b3-pre-tdo-heme-oxygen In the human TDO2 substrate complex, molecular oxygen was coordinated to the heme iron next to the L-tryptophan substrate. Condition category: normal nutrient_topic: Niacin research collection; topical membership is not evidence of a direct dietary effect. plain_language: Iron held in heme positions oxygen for this precursor reaction. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified human TDO2 crystallography and spectroscopy; substrate/product complexes limitations: Purified-enzyme evidence does not establish dietary intake requirements or clinical outcomes. exposure: Biochemical or structural assay; no dietary intervention cross_nutrient: Heme iron participates in a tryptophan-to-niacin upstream enzyme; the structure does not establish a dietary iron threshold. evidence_span: {"source_cache": "artifacts/niacin-precursors-sources/tdo2016.paragraphs.txt", "locator": "Normalized full-text paragraphs 7–7 (0-based)", "start_char": 5512, "end_char": 7250, "file_sha256": "3f91886745b8ff9fb808232c839dd346b03605dd025d5fa682a3de4f81338ec5", "text_sha256": "057137936657c739cdef730f5d10b930ec40af5e09f0ed4e2abbd813f26db9f0"} [b3-pre-tdo2016] Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase. (2016). https://pubmed.ncbi.nlm.nih.gov/27762317/ DOI: 10.1038/srep35169

cross_nutrient

Tryptophan provides the carbon framework entering the de novo niacin pathway; downstream steps remain necessary.

evidence_span

{"source_cache": "artifacts/niacin-precursors-sources/tdo2016.paragraphs.txt", "locator": "Normalized full-text paragraphs 9–9 (0-based)", "start_char": 8003, "end_char": 9136, "file_sha256": "3f91886745b8ff9fb808232c839dd346b03605dd025d5fa682a3de4f81338ec5", "text_sha256": "b39e2ce5d405e5eb8fde25aec369c306954365d7ec2b448fe5a5689e89785e2a"}

experimental_model

Purified human TDO2 crystallography and spectroscopy; substrate/product complexes

exposure

Biochemical or structural assay; no dietary intervention

limitations

Purified-enzyme evidence does not establish dietary intake requirements or clinical outcomes.

nutrient_topic

Niacin research collection; topical membership is not evidence of a direct dietary effect. · Niacin (vitamin B3)

organism

Homo sapiens

plain_language

TDO2 opens the tryptophan ring at the beginning of the kynurenine route.

primary_references

[b3-pre-tdo2016] Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase. (2016). https://pubmed.ncbi.nlm.nih.gov/27762317/ DOI: 10.1038/srep35169

tissue_or_cell_type

Purified recombinant protein; no intact tissue

Niacin: NAD metabolism, deficiency and nutrient interactions (2026-09-17) · lines 479–491

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human TDO2 crystallography and spectroscopy; substrate/product complexes · source_derived_draft · unverified_draft

### b3-pre-tdo-reaction Human TDO2 substrate and product structures support oxidative conversion of L-tryptophan and oxygen to N-formylkynurenine. Condition category: normal nutrient_topic: Niacin research collection; topical membership is not evidence of a direct dietary effect. plain_language: TDO2 opens the tryptophan ring at the beginning of the kynurenine route. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified human TDO2 crystallography and spectroscopy; substrate/product complexes limitations: Purified-enzyme evidence does not establish dietary intake requirements or clinical outcomes. exposure: Biochemical or structural assay; no dietary intervention cross_nutrient: Tryptophan provides the carbon framework entering the de novo niacin pathway; downstream steps remain necessary. evidence_span: {"source_cache": "artifacts/niacin-precursors-sources/tdo2016.paragraphs.txt", "locator": "Normalized full-text paragraphs 9–9 (0-based)", "start_char": 8003, "end_char": 9136, "file_sha256": "3f91886745b8ff9fb808232c839dd346b03605dd025d5fa682a3de4f81338ec5", "text_sha256": "b39e2ce5d405e5eb8fde25aec369c306954365d7ec2b448fe5a5689e89785e2a"} [b3-pre-tdo2016] Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase. (2016). https://pubmed.ncbi.nlm.nih.gov/27762317/ DOI: 10.1038/srep35169

evidence_span

{"source_cache": "artifacts/cold-research/9753429.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "3c76ec6d5dadb463c0a044175d5a78fbd02df4da7c339029c8c232e8878175b9", "start_char": 0, "end_char": 1695, "text_sha256": "3c76ec6d5dadb463c0a044175d5a78fbd02df4da7c339029c8c232e8878175b9"}

experimental_model

Crystal structure of rat tyrosine hydroxylase with a cofactor analogue and iron at 2.3 angstrom

exposure

Bound 7,8-dihydrobiopterin and iron

limitations

Structural chemistry of the rate-limiting step. It is a rat enzyme structure with a cofactor analogue, not a measurement of iron status in an animal.

nutrient_topic

Cold water immersion research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Cold water immersion

organism

Rat enzyme

plain_language

The first and slowest step of making noradrenaline needs an iron atom and a molecule of oxygen.

primary_references

[cold-p9753429] Crystal structure of tyrosine hydroxylase with bound cofactor analogue and iron at 2.3 A resolution: self-hydroxylation of Phe300 and the pterin-binding site. (1998). https://pubmed.ncbi.nlm.nih.gov/9753429/ DOI: 10.1021/bi981462g

tissue_or_cell_type

Purified catalytic and tetramerization domains

Cold water immersion: cold sensing, heat production, the catecholamine axis and what repeated exposure changes (2026-09-19) · lines 533–544

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Crystal structure of rat tyrosine hydroxylase with a cofactor analogue and iron at 2.3 angstrom · source_derived_draft · unverified_draft

### cold-th-iron-oxygen-pterin Tyrosine hydroxylase is a non-heme iron enzyme that uses molecular oxygen to hydroxylate tyrosine to L-DOPA and tetrahydrobiopterin to 4a-hydroxybiopterin in the rate-limiting step of the catecholamine biosynthetic pathway. Condition category: normal nutrient_topic: Cold water immersion research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: The first and slowest step of making noradrenaline needs an iron atom and a molecule of oxygen. organism: Rat enzyme tissue_or_cell_type: Purified catalytic and tetramerization domains experimental_model: Crystal structure of rat tyrosine hydroxylase with a cofactor analogue and iron at 2.3 angstrom limitations: Structural chemistry of the rate-limiting step. It is a rat enzyme structure with a cofactor analogue, not a measurement of iron status in an animal. exposure: Bound 7,8-dihydrobiopterin and iron evidence_span: {"source_cache": "artifacts/cold-research/9753429.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "3c76ec6d5dadb463c0a044175d5a78fbd02df4da7c339029c8c232e8878175b9", "start_char": 0, "end_char": 1695, "text_sha256": "3c76ec6d5dadb463c0a044175d5a78fbd02df4da7c339029c8c232e8878175b9"} [cold-p9753429] Crystal structure of tyrosine hydroxylase with bound cofactor analogue and iron at 2.3 A resolution: self-hydroxylation of Phe300 and the pterin-binding site. (1998). https://pubmed.ncbi.nlm.nih.gov/9753429/ DOI: 10.1021/bi981462g

evidence_span

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experimental_model

Crystal structure of rat tyrosine hydroxylase with a cofactor analogue and iron at 2.3 angstrom

exposure

Bound 7,8-dihydrobiopterin and iron

limitations

Structural chemistry of the rate-limiting step. It is a rat enzyme structure with a cofactor analogue, not a measurement of iron status in an animal.

nutrient_topic

Cold water immersion research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. · Cold water immersion

organism

Rat enzyme

plain_language

The oxygen molecule slots into the gap between the cofactor and the iron.

primary_references

[cold-p9753429] Crystal structure of tyrosine hydroxylase with bound cofactor analogue and iron at 2.3 A resolution: self-hydroxylation of Phe300 and the pterin-binding site. (1998). https://pubmed.ncbi.nlm.nih.gov/9753429/ DOI: 10.1021/bi981462g

tissue_or_cell_type

Purified catalytic and tetramerization domains

Cold water immersion: cold sensing, heat production, the catecholamine axis and what repeated exposure changes (2026-09-19) · lines 546–557

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Crystal structure of rat tyrosine hydroxylase with a cofactor analogue and iron at 2.3 angstrom · source_derived_draft · unverified_draft

### cold-th-pterin-geometry The pterin binds in the active-site cleft forming an aromatic stacking interaction with Phe300, which is itself hydroxylated in the meta position by an autocatalytic process and anchored by a hydrogen bond to the carbonyl of Gln310; the iron sits 5.6 angstrom from the pterin 4a carbon, and molecular oxygen could bind in a bridging position between the pterin and the iron before substrate hydroxylation. Condition category: normal nutrient_topic: Cold water immersion research collection; topical membership is not evidence of a direct clinical effect, and a therapeutic exposure is not a dietary intake. plain_language: The oxygen molecule slots into the gap between the cofactor and the iron. organism: Rat enzyme tissue_or_cell_type: Purified catalytic and tetramerization domains experimental_model: Crystal structure of rat tyrosine hydroxylase with a cofactor analogue and iron at 2.3 angstrom limitations: Structural chemistry of the rate-limiting step. It is a rat enzyme structure with a cofactor analogue, not a measurement of iron status in an animal. exposure: Bound 7,8-dihydrobiopterin and iron evidence_span: {"source_cache": "artifacts/cold-research/9753429.abstract.txt", "locator": "Indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "3c76ec6d5dadb463c0a044175d5a78fbd02df4da7c339029c8c232e8878175b9", "start_char": 0, "end_char": 1695, "text_sha256": "3c76ec6d5dadb463c0a044175d5a78fbd02df4da7c339029c8c232e8878175b9"} [cold-p9753429] Crystal structure of tyrosine hydroxylase with bound cofactor analogue and iron at 2.3 A resolution: self-hydroxylation of Phe300 and the pterin-binding site. (1998). https://pubmed.ncbi.nlm.nih.gov/9753429/ DOI: 10.1021/bi981462g

experimental_model

Redox-controlled neutron structures of human SOD2

exposure

Redox-controlled Mn(III) and Mn(II) crystals

limitations

Primary experimental scope only; no human dietary threshold, clinical treatment rule, or universal metal substitution is established.

nutrient_topic

Manganese research collection; topical membership is not evidence of a direct dietary effect. · Manganese

organism

Homo sapiens

plain_language

SOD2 removes superoxide; it produces hydrogen peroxide that requires further handling.

primary_references

[mn-enz-33824320] Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase. (2021). https://pubmed.ncbi.nlm.nih.gov/33824320/ DOI: 10.1038/s41467-021-22290-1

tissue_or_cell_type

Purified enzyme; mitochondrial-matrix protein

Manganese: enzyme cofactors, glycosylation, transport and nutrient interactions (2026-09-17) · lines 446–456

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Redox-controlled neutron structures of human SOD2 · source_derived_draft · unverified_draft

### mn-enz-sod2-superoxide Human SOD2 uses a Mn(III)/Mn(II) cycle to convert superoxide into oxygen and hydrogen peroxide. Condition category: normal nutrient_topic: Manganese research collection; topical membership is not evidence of a direct dietary effect. plain_language: SOD2 removes superoxide; it produces hydrogen peroxide that requires further handling. organism: Homo sapiens tissue_or_cell_type: Purified enzyme; mitochondrial-matrix protein experimental_model: Redox-controlled neutron structures of human SOD2 limitations: Primary experimental scope only; no human dietary threshold, clinical treatment rule, or universal metal substitution is established. exposure: Redox-controlled Mn(III) and Mn(II) crystals [mn-enz-33824320] Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase. (2021). https://pubmed.ncbi.nlm.nih.gov/33824320/ DOI: 10.1038/s41467-021-22290-1

experimental_model

Human cDNA expression and human tissue activity assays

limitations

Do not generalize full carnitine-synthesis capacity to every tissue.

organism

Homo sapiens

plain_language

BBOX1 completes carnitine synthesis.

primary_references

[vaz1998] Carnitine biosynthesis: identification of the cDNA encoding human gamma-butyrobetaine hydroxylase (1998). https://pubmed.ncbi.nlm.nih.gov/9753662/ DOI: 10.1006/bbrc.1998.9343 [rebouche1980] Tissue distribution of carnitine biosynthetic enzymes in man (1980). https://pubmed.ncbi.nlm.nih.gov/6770910/ DOI: 10.1016/0304-4165(80)90133-6

tissue_or_cell_type

Kidney, liver and brain; abundance differs

L-Lysine: mechanism-first literature curation (2026-09-17) · lines 207–216

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human cDNA expression and human tissue activity assays · source_derived_draft · unverified_draft

### bbox1-carnitine-formation BBOX1 hydroxylates gamma-butyrobetaine to L-carnitine using oxygen, 2-oxoglutarate and ferrous iron. Plain language: BBOX1 completes carnitine synthesis. Condition category: normal organism: Homo sapiens tissue_or_cell_type: Kidney, liver and brain; abundance differs experimental_model: Human cDNA expression and human tissue activity assays limitations: Do not generalize full carnitine-synthesis capacity to every tissue. [vaz1998] Carnitine biosynthesis: identification of the cDNA encoding human gamma-butyrobetaine hydroxylase (1998). https://pubmed.ncbi.nlm.nih.gov/9753662/ DOI: 10.1006/bbrc.1998.9343 [rebouche1980] Tissue distribution of carnitine biosynthetic enzymes in man (1980). https://pubmed.ncbi.nlm.nih.gov/6770910/ DOI: 10.1016/0304-4165(80)90133-6

experimental_model

Human DOHH structures and spectroscopy.

limitations

DOHH is a diiron enzyme, not a 2-oxoglutarate-dependent hydroxylase. This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome.

organism

Human

plain_language

A second enzyme completes the special modification.

primary_references

[dohh-2015] Crystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination (2015). https://pubmed.ncbi.nlm.nih.gov/25865244/ DOI: 10.1016/j.str.2015.03.002

tissue_or_cell_type

Not specified as a whole tissue; see experimental model.

L-Lysine: mechanism-first literature curation (2026-09-17) · lines 588–596

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human DOHH structures and spectroscopy. · source_derived_draft · unverified_draft

### dohh-eif5a-hypusine DOHH hydroxylates deoxyhypusine-eIF5A to hypusine-eIF5A using its oxygen-activating diiron center. Plain language: A second enzyme completes the special modification. Condition category: normal organism: Human tissue_or_cell_type: Not specified as a whole tissue; see experimental model. experimental_model: Human DOHH structures and spectroscopy. limitations: DOHH is a diiron enzyme, not a 2-oxoglutarate-dependent hydroxylase. This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome. [dohh-2015] Crystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination (2015). https://pubmed.ncbi.nlm.nih.gov/25865244/ DOI: 10.1016/j.str.2015.03.002

experimental_model

Purified LSD1 enzyme / histone assays and cellular RNA interference.

limitations

Do not extend this specific activity to trimethyllysine or every histone site. This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome.

organism

Human

plain_language

Some lysine methyl marks can be erased by a flavin enzyme.

primary_references

[lsd1-2004] Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 (2004). https://pubmed.ncbi.nlm.nih.gov/15620353/ DOI: 10.1016/j.cell.2004.12.012

tissue_or_cell_type

Not specified as a whole tissue; see experimental model.

L-Lysine: mechanism-first literature curation (2026-09-17) · lines 557–565

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified LSD1 enzyme / histone assays and cellular RNA interference. · source_derived_draft · unverified_draft

### kdm1a-h3k4-demethylation KDM1A/LSD1 oxidatively removes a methyl group from H3K4me2 through a flavin-dependent reaction. Plain language: Some lysine methyl marks can be erased by a flavin enzyme. Condition category: normal organism: Human tissue_or_cell_type: Not specified as a whole tissue; see experimental model. experimental_model: Purified LSD1 enzyme / histone assays and cellular RNA interference. limitations: Do not extend this specific activity to trimethyllysine or every histone site. This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome. [lsd1-2004] Histone demethylation mediated by the nuclear amine oxidase homolog LSD1 (2004). https://pubmed.ncbi.nlm.nih.gov/15620353/ DOI: 10.1016/j.cell.2004.12.012

experimental_model

Human JMJD2A catalytic-domain structures and methylated peptide assays.

limitations

This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome.

organism

Human

plain_language

An iron-dependent enzyme erases a different class of methyl mark.

primary_references

[kdm4a-2006] Structural insights into histone demethylation by JMJD2 family members (2006). https://pubmed.ncbi.nlm.nih.gov/16677698/ DOI: 10.1016/j.cell.2006.04.024 [kdm4a-specificity-2007] Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase (2007). https://pubmed.ncbi.nlm.nih.gov/17589523/ DOI: 10.1038/nsmb1273

tissue_or_cell_type

Not specified as a whole tissue; see experimental model.

L-Lysine: mechanism-first literature curation (2026-09-17) · lines 567–576

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human JMJD2A catalytic-domain structures and methylated peptide assays. · source_derived_draft · unverified_draft

### kdm4a-h3k9-demethylation KDM4A/JMJD2A can convert H3K9me3 to H3K9me2 using Fe(II), oxygen and 2-oxoglutarate. Plain language: An iron-dependent enzyme erases a different class of methyl mark. Condition category: normal organism: Human tissue_or_cell_type: Not specified as a whole tissue; see experimental model. experimental_model: Human JMJD2A catalytic-domain structures and methylated peptide assays. limitations: This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome. [kdm4a-2006] Structural insights into histone demethylation by JMJD2 family members (2006). https://pubmed.ncbi.nlm.nih.gov/16677698/ DOI: 10.1016/j.cell.2006.04.024 [kdm4a-specificity-2007] Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase (2007). https://pubmed.ncbi.nlm.nih.gov/17589523/ DOI: 10.1038/nsmb1273

experimental_model

LOXL2 assay development and total-family activity detection in cultured cells and tissue.

limitations

Substrate sites and enzyme-family members differ; peroxide production alone does not establish systemic oxidative injury.

organism

Mammalian cells/tissues and recombinant LOXL2; see study methods

plain_language

An enzyme creates reactive attachment sites used in matrix cross-linking.

primary_references

[lox-assay-2021] An in situ activity assay for lysyl oxidases (2021). https://pubmed.ncbi.nlm.nih.gov/34226627/

tissue_or_cell_type

Not specified as a whole tissue; see experimental model.

L-Lysine: mechanism-first literature curation (2026-09-17) · lines 467–475

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · LOXL2 assay development and total-family activity detection in cultured cells and tissue. · source_derived_draft · unverified_draft

### lox-peptidyl-lysine-oxidation Lysyl oxidase converts suitable peptidyl lysines to allysine, producing ammonia and hydrogen peroxide. Plain language: An enzyme creates reactive attachment sites used in matrix cross-linking. Condition category: normal organism: Mammalian cells/tissues and recombinant LOXL2; see study methods tissue_or_cell_type: Not specified as a whole tissue; see experimental model. experimental_model: LOXL2 assay development and total-family activity detection in cultured cells and tissue. limitations: Substrate sites and enzyme-family members differ; peroxide production alone does not establish systemic oxidative injury. [lox-assay-2021] An in situ activity assay for lysyl oxidases (2021). https://pubmed.ncbi.nlm.nih.gov/34226627/

experimental_model

Recombinant human PLOD3 structural and biochemical assays.

limitations

This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome.

organism

Human

plain_language

The collagen enzyme needs an iron-containing catalytic site and reaction partners.

primary_references

[plod3-2018] Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 (2018). https://www.nature.com/articles/s41467-018-05631-5 DOI: 10.1038/s41467-018-05631-5

tissue_or_cell_type

Not specified as a whole tissue; see experimental model.

L-Lysine: mechanism-first literature curation (2026-09-17) · lines 417–425

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human PLOD3 structural and biochemical assays. · source_derived_draft · unverified_draft

### plod3-collagen-hydroxylation PLOD3 hydroxylates peptidyl lysine using Fe(II), 2-oxoglutarate and oxygen. Plain language: The collagen enzyme needs an iron-containing catalytic site and reaction partners. Condition category: normal organism: Human tissue_or_cell_type: Not specified as a whole tissue; see experimental model. experimental_model: Recombinant human PLOD3 structural and biochemical assays. limitations: This reaction modifies lysine already in a protein. It does not show that extra oral lysine increases the reaction or improves a clinical outcome. [plod3-2018] Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3 (2018). https://www.nature.com/articles/s41467-018-05631-5 DOI: 10.1038/s41467-018-05631-5

experimental_model

Recombinant human TMLH, synthetic standards and NMR; Recombinant human TMLH and substrate analogue assays

limitations

The substrate is free trimethyllysine after proteolysis, not ordinary free lysine.

organism

Homo sapiens

plain_language

TMLHE begins conversion of released trimethyllysine toward carnitine.

primary_references

[lesniak2017] Human carnitine biosynthesis proceeds via (2S,3S)-3-hydroxy-Nε-trimethyllysine (2017). https://pmc.ncbi.nlm.nih.gov/articles/PMC5644716/ DOI: 10.1039/C6CC08381A [tmlh2016scope] Substrate scope for trimethyllysine hydroxylase catalysis (2016). https://pubs.rsc.org/en/content/articlehtml/2016/cc/c6cc07845a DOI: 10.1039/C6CC07845A

tissue_or_cell_type

Mitochondrial carnitine-biosynthesis step

L-Lysine: mechanism-first literature curation (2026-09-17) · lines 166–175

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human TMLH, synthetic standards and NMR; Recombinant human TMLH and substrate analogue assays · source_derived_draft · unverified_draft

### tmlhe-hydroxylation Human TMLHE hydroxylates free trimethyllysine to (2S,3S)-hydroxytrimethyllysine, coupled to 2-oxoglutarate oxidation. Plain language: TMLHE begins conversion of released trimethyllysine toward carnitine. Condition category: normal organism: Homo sapiens tissue_or_cell_type: Mitochondrial carnitine-biosynthesis step experimental_model: Recombinant human TMLH, synthetic standards and NMR; Recombinant human TMLH and substrate analogue assays limitations: The substrate is free trimethyllysine after proteolysis, not ordinary free lysine. [lesniak2017] Human carnitine biosynthesis proceeds via (2S,3S)-3-hydroxy-Nε-trimethyllysine (2017). https://pmc.ncbi.nlm.nih.gov/articles/PMC5644716/ DOI: 10.1039/C6CC08381A [tmlh2016scope] Substrate scope for trimethyllysine hydroxylase catalysis (2016). https://pubs.rsc.org/en/content/articlehtml/2016/cc/c6cc07845a DOI: 10.1039/C6CC07845A

cross_nutrient

true

evidence_location

Figure 2a–b; Oximetry Methods

experimental_model

Cell-free medium oximetry; peroxide inferred from catalase-triggered oxygen release

exposure

5 mM ascorbate ±5 µM FAC iron; oxygen trace and 600 U catalase addition after about 15 min.

limitations

FAC supplementation changes iron speciation as well as concentration; matching plasma total iron does not reconstruct transferrin binding or tissue interstitial chemistry. No clinical efficacy conclusion. The endpoint measures net peroxide and does not separately determine every elementary redox rate.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Cell-free bovine-serum-containing medium

plain_language

Iron sped up vitamin C oxidation while also helping remove the peroxide produced.

primary_references

[c-reg-mojic] Extracellular iron diminishes anticancer effects of vitamin C: an in vitro study. (2014). https://pubmed.ncbi.nlm.nih.gov/25092529/ DOI: 10.1038/srep05955

tissue_or_cell_type

RPMI-1640 +10% FCS

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1299–1311

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Cell-free medium oximetry; peroxide inferred from catalase-triggered oxygen release · source_derived_draft · unverified_draft

### c-reg-extracellular-iron-peroxide-removal In RPMI/FCS exposed to 5 mM ascorbate, added 5 µM FAC iron accelerated oxygen consumption/ascorbate oxidation but reduced detectable peroxide accumulation, showing that faster oxidation need not yield a larger steady peroxide pool. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Iron sped up vitamin C oxidation while also helping remove the peroxide produced. organism: Cell-free bovine-serum-containing medium tissue_or_cell_type: RPMI-1640 +10% FCS experimental_model: Cell-free medium oximetry; peroxide inferred from catalase-triggered oxygen release limitations: FAC supplementation changes iron speciation as well as concentration; matching plasma total iron does not reconstruct transferrin binding or tissue interstitial chemistry. No clinical efficacy conclusion. The endpoint measures net peroxide and does not separately determine every elementary redox rate. exposure: 5 mM ascorbate ±5 µM FAC iron; oxygen trace and 600 U catalase addition after about 15 min. cross_nutrient: true evidence_location: Figure 2a–b; Oximetry Methods [c-reg-mojic] Extracellular iron diminishes anticancer effects of vitamin C: an in vitro study. (2014). https://pubmed.ncbi.nlm.nih.gov/25092529/ DOI: 10.1038/srep05955

cross_nutrient

true

evidence_location

Primary abstract rate/extent and substrate comparisons

experimental_model

Purified enzyme with human HIF-1 alpha-derived peptide substrate

exposure

Ascorbate versus omission/alternative reducing agents; exact concentrations and enzyme constructs not recovered from primary abstract.

limitations

Peptide hydroxylation does not directly establish HIF degradation or transcription changes in intact cells; ankyrin probe is not physiological HIF.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Human HIF-1 alpha substrate; purified recombinant hydroxylase

plain_language

Vitamin C also supported a different HIF enzyme that modifies an asparagine site.

primary_references

[c-reg-flashman] Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents. (2010). https://pubmed.ncbi.nlm.nih.gov/20055761/ DOI: 10.1042/bj20091609

tissue_or_cell_type

Cell-free

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1131–1143

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified enzyme with human HIF-1 alpha-derived peptide substrate · source_derived_draft · unverified_draft

### c-reg-fih-ascorbate Ascorbate increased the initial rate and extent of FIH-catalyzed asparaginyl hydroxylation of human HIF-1 alpha peptide; the study separately tested a consensus ankyrin-repeat peptide. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C also supported a different HIF enzyme that modifies an asparagine site. organism: Human HIF-1 alpha substrate; purified recombinant hydroxylase tissue_or_cell_type: Cell-free experimental_model: Purified enzyme with human HIF-1 alpha-derived peptide substrate limitations: Peptide hydroxylation does not directly establish HIF degradation or transcription changes in intact cells; ankyrin probe is not physiological HIF. exposure: Ascorbate versus omission/alternative reducing agents; exact concentrations and enzyme constructs not recovered from primary abstract. cross_nutrient: true evidence_location: Primary abstract rate/extent and substrate comparisons [c-reg-flashman] Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents. (2010). https://pubmed.ncbi.nlm.nih.gov/20055761/ DOI: 10.1042/bj20091609

availability_state

nutrient_deficiency Imported condition classification; unverified.

cross_nutrient

false

evidence_location

Figure 5C–D; Animal studies

experimental_model

Dietary withdrawal in adult male Gulo-null mice with supplemented-genotype controls

exposure

Maintenance 0.33 g/L ascorbic acid drinking water; withdrawal about 35–36 days; 8% inspired oxygen for 24 h.

limitations

Dietary deficiency in a synthesis-null animal; does not establish that every HIF target or tissue is unaffected, nor a safe human deficiency threshold.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Mus musculus

plain_language

Even severely vitamin-C-depleted mice retained this measured hormonal response to low oxygen.

primary_references

[c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

tissue_or_cell_type

Plasma erythropoietin; kidney Epo mRNA supporting endpoint

trigger_kind

nutrient_deficiency Imported condition classification; unverified.

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1187–1199

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Dietary withdrawal in adult male Gulo-null mice with supplemented-genotype controls · source_derived_draft · unverified_draft

### c-reg-gulo-depletion-epo-preserved Male Gulo-null mice deprived of vitamin C for approximately five weeks retained a robust plasma erythropoietin response to 24 h at 8% oxygen, similar to supplemented controls, despite plasma ascorbate at or below 1 µM and scorbutic weight loss. Condition category: nutrient_deficiency nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Even severely vitamin-C-depleted mice retained this measured hormonal response to low oxygen. organism: Mus musculus tissue_or_cell_type: Plasma erythropoietin; kidney Epo mRNA supporting endpoint experimental_model: Dietary withdrawal in adult male Gulo-null mice with supplemented-genotype controls limitations: Dietary deficiency in a synthesis-null animal; does not establish that every HIF target or tissue is unaffected, nor a safe human deficiency threshold. exposure: Maintenance 0.33 g/L ascorbic acid drinking water; withdrawal about 35–36 days; 8% inspired oxygen for 24 h. cross_nutrient: false evidence_location: Figure 5C–D; Animal studies [c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

availability_state

nutrient_deficiency Imported condition classification; unverified.

cross_nutrient

false

evidence_location

Figure 1B–C

experimental_model

HeLa adapted to serum-free Ham F-12; HIF immunoblot and luciferase reporter

exposure

0 versus 50 µM ascorbate; 0.2% versus 21% oxygen for 6-h protein assay, graded oxygen for 24-h reporter assay.

limitations

Cell-culture omission, not a controlled human dietary deficiency; residual adaptive reductant pathways were not eliminated.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Homo sapiens

plain_language

Removing vitamin C from this adapted cancer-cell culture did not switch off its measured low-oxygen response.

primary_references

[c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

tissue_or_cell_type

Cervical carcinoma cells

trigger_kind

nutrient_deficiency Imported condition classification; unverified.

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1173–1185

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · HeLa adapted to serum-free Ham F-12; HIF immunoblot and luciferase reporter · source_derived_draft · unverified_draft

### c-reg-hela-hypoxia-preserved HeLa cells maintained in serum-free, ascorbate-free defined medium retained hypoxic HIF-1 alpha stabilization and HIF-dependent reporter activation relative to cells supplied with 50 µM ascorbate. Condition category: nutrient_deficiency nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Removing vitamin C from this adapted cancer-cell culture did not switch off its measured low-oxygen response. organism: Homo sapiens tissue_or_cell_type: Cervical carcinoma cells experimental_model: HeLa adapted to serum-free Ham F-12; HIF immunoblot and luciferase reporter limitations: Cell-culture omission, not a controlled human dietary deficiency; residual adaptive reductant pathways were not eliminated. exposure: 0 versus 50 µM ascorbate; 0.2% versus 21% oxygen for 6-h protein assay, graded oxygen for 24-h reporter assay. cross_nutrient: false evidence_location: Figure 1B–C [c-reg-nytko] Vitamin C is dispensable for oxygen sensing in vivo. (2011). https://pubmed.ncbi.nlm.nih.gov/21346252/ DOI: 10.1182/blood-2010-09-307637

cross_nutrient

false

evidence_location

Figure 4A–C

experimental_model

Cell-free medium; catalase-dependent oxygen-electrode peroxide assay and EPR

exposure

0.2–2 mM ascorbate over 1 h; 2 mM ascorbate with 0.5–10% FBS in serum-dependence experiment.

limitations

Pharmacological in-vitro exposure; medium chemistry and peroxide clearance differ from intact tissues. No dietary or clinical anticancer inference. Net accumulation reflects both production and removal; ascorbate can interfere with routine peroxidase assays.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Cell-free; bovine serum-containing medium

plain_language

The culture liquid itself could turn high-concentration vitamin C into peroxide.

primary_references

[c-reg-chen] Pharmacologic ascorbic acid concentrations selectively kill cancer cells: action as a pro-drug to deliver hydrogen peroxide to tissues. (2005). https://pubmed.ncbi.nlm.nih.gov/16157892/ DOI: 10.1073/pnas.0506390102

tissue_or_cell_type

Extracellular assay medium

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1257–1269

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Cell-free medium; catalase-dependent oxygen-electrode peroxide assay and EPR · source_derived_draft · unverified_draft

### c-reg-medium-peroxide-generation Ascorbate produced peroxide in cell culture medium without requiring cells; accumulation depended on ascorbate concentration, time and serum fraction, and tracked ascorbyl radical detected by EPR. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: The culture liquid itself could turn high-concentration vitamin C into peroxide. organism: Cell-free; bovine serum-containing medium tissue_or_cell_type: Extracellular assay medium experimental_model: Cell-free medium; catalase-dependent oxygen-electrode peroxide assay and EPR limitations: Pharmacological in-vitro exposure; medium chemistry and peroxide clearance differ from intact tissues. No dietary or clinical anticancer inference. Net accumulation reflects both production and removal; ascorbate can interfere with routine peroxidase assays. exposure: 0.2–2 mM ascorbate over 1 h; 2 mM ascorbate with 0.5–10% FBS in serum-dependence experiment. cross_nutrient: false evidence_location: Figure 4A–C [c-reg-chen] Pharmacologic ascorbic acid concentrations selectively kill cancer cells: action as a pro-drug to deliver hydrogen peroxide to tissues. (2005). https://pubmed.ncbi.nlm.nih.gov/16157892/ DOI: 10.1073/pnas.0506390102

cross_nutrient

true

evidence_location

Primary abstract rate/extent and substrate comparisons

experimental_model

Purified enzyme with human HIF-1 alpha-derived peptide substrate

exposure

Ascorbate versus omission/alternative reducing agents; exact concentrations and enzyme constructs not recovered from primary abstract.

limitations

Peptide hydroxylation does not directly establish HIF degradation or transcription changes in intact cells; ankyrin probe is not physiological HIF.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Human HIF-1 alpha substrate; purified recombinant hydroxylase

plain_language

Vitamin C increased the activity of an isolated oxygen-sensing proline hydroxylase.

primary_references

[c-reg-flashman] Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents. (2010). https://pubmed.ncbi.nlm.nih.gov/20055761/ DOI: 10.1042/bj20091609

tissue_or_cell_type

Cell-free

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1117–1129

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified enzyme with human HIF-1 alpha-derived peptide substrate · source_derived_draft · unverified_draft

### c-reg-phd2-ascorbate Ascorbate increased the initial rate and extent of PHD2-catalyzed hydroxylation at both tested human HIF-1 alpha prolyl sites in purified-enzyme peptide experiments. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C increased the activity of an isolated oxygen-sensing proline hydroxylase. organism: Human HIF-1 alpha substrate; purified recombinant hydroxylase tissue_or_cell_type: Cell-free experimental_model: Purified enzyme with human HIF-1 alpha-derived peptide substrate limitations: Peptide hydroxylation does not directly establish HIF degradation or transcription changes in intact cells; ankyrin probe is not physiological HIF. exposure: Ascorbate versus omission/alternative reducing agents; exact concentrations and enzyme constructs not recovered from primary abstract. cross_nutrient: true evidence_location: Primary abstract rate/extent and substrate comparisons [c-reg-flashman] Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents. (2010). https://pubmed.ncbi.nlm.nih.gov/20055761/ DOI: 10.1042/bj20091609

cross_nutrient

Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing.

experimental_model

Rat pituitary and bovine intermediate-pituitary secretory-granule preparations

exposure

Synthetic D-Tyr-Val-Gly amidation with varied ascorbate, oxygen and divalent-metal chelators/copper.

limitations

Study included rat and bovine preparations; this cofactor observation is scoped to those preparations rather than a human nutritional copper trial.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Rattus norvegicus; Bos taurus

plain_language

Vitamin C and copper participate together, and removing available metal stops this peptide-processing assay.

primary_references

[pam1983] Identification in pituitary tissue of a peptide alpha-amidation activity that acts on glycine-extended peptides and requires molecular oxygen, copper, and ascorbic acid. (1983). https://pubmed.ncbi.nlm.nih.gov/6576381/ DOI: 10.1073/pnas.80.16.5144

tissue_or_cell_type

Pituitary secretory granules

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 872–883

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Rat pituitary and bovine intermediate-pituitary secretory-granule preparations · source_derived_draft · unverified_draft

### vc-enzyme-amidation-copper-recovery Pituitary peptide-amidating activity inhibited by divalent-metal chelators was restored above control by copper addition; the assayed reaction also required molecular oxygen. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C and copper participate together, and removing available metal stops this peptide-processing assay. organism: Rattus norvegicus; Bos taurus tissue_or_cell_type: Pituitary secretory granules experimental_model: Rat pituitary and bovine intermediate-pituitary secretory-granule preparations limitations: Study included rat and bovine preparations; this cofactor observation is scoped to those preparations rather than a human nutritional copper trial. cross_nutrient: Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing. exposure: Synthetic D-Tyr-Val-Gly amidation with varied ascorbate, oxygen and divalent-metal chelators/copper. [pam1983] Identification in pituitary tissue of a peptide alpha-amidation activity that acts on glycine-extended peptides and requires molecular oxygen, copper, and ascorbic acid. (1983). https://pubmed.ncbi.nlm.nih.gov/6576381/ DOI: 10.1073/pnas.80.16.5144

cross_nutrient

Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing.

experimental_model

Bovine intermediate-pituitary secretory-granule kinetic assay

exposure

Synthetic D-Tyr-Val-Gly amidation with varied ascorbate, oxygen and divalent-metal chelators/copper.

limitations

The old granule preparation is not a purified modern PAM-domain assay; synthetic substrate kinetics do not quantify all hormone amidation.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Bos taurus

plain_language

Vitamin C helps the pituitary enzyme finish a peptide with an amide group.

primary_references

[pam1983] Identification in pituitary tissue of a peptide alpha-amidation activity that acts on glycine-extended peptides and requires molecular oxygen, copper, and ascorbic acid. (1983). https://pubmed.ncbi.nlm.nih.gov/6576381/ DOI: 10.1073/pnas.80.16.5144

tissue_or_cell_type

Pituitary secretory granules

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 859–870

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Bovine intermediate-pituitary secretory-granule kinetic assay · source_derived_draft · unverified_draft

### vc-enzyme-bovine-amidation-ascorbate Bovine intermediate-pituitary granule amidation of D-Tyr-Val-Gly responded to ascorbate, with apparent substrate Km and Vmax changing as the ascorbate concentration changed. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C helps the pituitary enzyme finish a peptide with an amide group. organism: Bos taurus tissue_or_cell_type: Pituitary secretory granules experimental_model: Bovine intermediate-pituitary secretory-granule kinetic assay limitations: The old granule preparation is not a purified modern PAM-domain assay; synthetic substrate kinetics do not quantify all hormone amidation. cross_nutrient: Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing. exposure: Synthetic D-Tyr-Val-Gly amidation with varied ascorbate, oxygen and divalent-metal chelators/copper. [pam1983] Identification in pituitary tissue of a peptide alpha-amidation activity that acts on glycine-extended peptides and requires molecular oxygen, copper, and ascorbic acid. (1983). https://pubmed.ncbi.nlm.nih.gov/6576381/ DOI: 10.1073/pnas.80.16.5144

cross_nutrient

Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing.

experimental_model

Purified chick prolyl and partially purified lysyl collagen hydroxylases

exposure

Peptide substrate present or absent; uncoupled 2-oxoglutarate decarboxylation assays.

limitations

This statement concerns coupled turnover; it must not be transferred to copper monooxygenases.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Gallus gallus

plain_language

Vitamin C is not a one-for-one consumed ingredient in every successful collagen hydroxylation.

primary_references

[myllyla1984] Ascorbate is consumed stoichiometrically in the uncoupled reactions catalyzed by prolyl 4-hydroxylase and lysyl hydroxylase. (1984). https://pubmed.ncbi.nlm.nih.gov/6325436/ DOI: 10.1016/s0021-9258(18)91023-9

tissue_or_cell_type

Chick embryo enzyme preparations

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 585–596

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified chick prolyl and partially purified lysyl collagen hydroxylases · source_derived_draft · unverified_draft

### vc-enzyme-coupled-ascorbate-use In chick collagen hydroxylase assays, complete proline hydroxylation was coupled to 2-oxoglutarate decarboxylation while ascorbate was not consumed in most catalytic cycles. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C is not a one-for-one consumed ingredient in every successful collagen hydroxylation. organism: Gallus gallus tissue_or_cell_type: Chick embryo enzyme preparations experimental_model: Purified chick prolyl and partially purified lysyl collagen hydroxylases limitations: This statement concerns coupled turnover; it must not be transferred to copper monooxygenases. cross_nutrient: Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing. exposure: Peptide substrate present or absent; uncoupled 2-oxoglutarate decarboxylation assays. [myllyla1984] Ascorbate is consumed stoichiometrically in the uncoupled reactions catalyzed by prolyl 4-hydroxylase and lysyl hydroxylase. (1984). https://pubmed.ncbi.nlm.nih.gov/6325436/ DOI: 10.1016/s0021-9258(18)91023-9

cross_nutrient

Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing.

experimental_model

Purified chick-embryo collagen prolyl hydroxylase kinetics

exposure

Ascorbate omitted or added in purified-enzyme assays; initial 5–10 seconds versus approximately 1 minute.

limitations

Purified assay with cofactor omission; does not quantify a dietary requirement or establish an identical turnover number in human cells.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Gallus gallus

plain_language

The collagen enzyme can start working without vitamin C, but sustained work needs vitamin C support.

primary_references

[myllyla1978] The role of ascorbate in the prolyl hydroxylase reaction. (1978). https://pubmed.ncbi.nlm.nih.gov/212056/ DOI: 10.1016/0006-291x(78)91010-0

tissue_or_cell_type

Chick embryo enzyme preparation

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 572–583

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified chick-embryo collagen prolyl hydroxylase kinetics · source_derived_draft · unverified_draft

### vc-enzyme-initial-p4h-turnover Purified chick collagen prolyl hydroxylase completed approximately 15–30 rapid catalytic cycles in 5–10 seconds without added ascorbate before activity declined. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: The collagen enzyme can start working without vitamin C, but sustained work needs vitamin C support. organism: Gallus gallus tissue_or_cell_type: Chick embryo enzyme preparation experimental_model: Purified chick-embryo collagen prolyl hydroxylase kinetics limitations: Purified assay with cofactor omission; does not quantify a dietary requirement or establish an identical turnover number in human cells. cross_nutrient: Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing. exposure: Ascorbate omitted or added in purified-enzyme assays; initial 5–10 seconds versus approximately 1 minute. [myllyla1978] The role of ascorbate in the prolyl hydroxylase reaction. (1978). https://pubmed.ncbi.nlm.nih.gov/212056/ DOI: 10.1016/0006-291x(78)91010-0

cross_nutrient

Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing.

experimental_model

Purified chick prolyl and partially purified lysyl collagen hydroxylases

exposure

Peptide substrate present or absent; uncoupled 2-oxoglutarate decarboxylation assays.

limitations

Substrate-free enzyme reaction; frequency and quantitative vitamin C cost of uncoupled cycles in human tissues were not measured.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Gallus gallus

plain_language

Vitamin C is consumed when this collagen enzyme runs a reaction cycle without hydroxylating its peptide target.

primary_references

[myllyla1984] Ascorbate is consumed stoichiometrically in the uncoupled reactions catalyzed by prolyl 4-hydroxylase and lysyl hydroxylase. (1984). https://pubmed.ncbi.nlm.nih.gov/6325436/ DOI: 10.1016/s0021-9258(18)91023-9

tissue_or_cell_type

Chick embryo enzyme preparations

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 611–622

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified chick prolyl and partially purified lysyl collagen hydroxylases · source_derived_draft · unverified_draft

### vc-enzyme-lysyl-uncoupled-consumption Chick collagen lysyl hydroxylase consumed ascorbate stoichiometrically during uncoupled 2-oxoglutarate decarboxylation in the absence of peptide substrate. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C is consumed when this collagen enzyme runs a reaction cycle without hydroxylating its peptide target. organism: Gallus gallus tissue_or_cell_type: Chick embryo enzyme preparations experimental_model: Purified chick prolyl and partially purified lysyl collagen hydroxylases limitations: Substrate-free enzyme reaction; frequency and quantitative vitamin C cost of uncoupled cycles in human tissues were not measured. cross_nutrient: Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing. exposure: Peptide substrate present or absent; uncoupled 2-oxoglutarate decarboxylation assays. [myllyla1984] Ascorbate is consumed stoichiometrically in the uncoupled reactions catalyzed by prolyl 4-hydroxylase and lysyl hydroxylase. (1984). https://pubmed.ncbi.nlm.nih.gov/6325436/ DOI: 10.1016/s0021-9258(18)91023-9

cross_nutrient

Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing.

experimental_model

Purified bovine pituitary PAL and bovine-domain expression constructs in HEK293 cells

exposure

Purified PAL with N-acetyl-Tyr-Val-alpha-hydroxyglycine; PHM or PAL-containing constructs expressed in HEK293.

limitations

Bovine protein expressed in human cells is not a human PAM protein; domain construct activity does not quantify tissue hormone synthesis.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Bos taurus (protein); Homo sapiens (expression host)

plain_language

Peptide amidation begins with a separate vitamin-C-dependent hydroxylation step.

primary_references

[pal1991] Peptidyl-alpha-hydroxyglycine alpha-amidating lyase. Purification, characterization, and expression. (1991). https://pubmed.ncbi.nlm.nih.gov/1902227/ DOI: 10.1016/s0021-9258(20)89524-6

tissue_or_cell_type

Bovine neurointermediate pituitary; heterologous HEK293

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 885–896

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified bovine pituitary PAL and bovine-domain expression constructs in HEK293 cells · source_derived_draft · unverified_draft

### vc-enzyme-pam-two-domains Expression of the bovine PHM-only construct in HEK293 cells increased secreted PHM activity, demonstrating a functional hydroxylating domain separable from the PAL portion of PAM. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Peptide amidation begins with a separate vitamin-C-dependent hydroxylation step. organism: Bos taurus (protein); Homo sapiens (expression host) tissue_or_cell_type: Bovine neurointermediate pituitary; heterologous HEK293 experimental_model: Purified bovine pituitary PAL and bovine-domain expression constructs in HEK293 cells limitations: Bovine protein expressed in human cells is not a human PAM protein; domain construct activity does not quantify tissue hormone synthesis. cross_nutrient: Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing. exposure: Purified PAL with N-acetyl-Tyr-Val-alpha-hydroxyglycine; PHM or PAL-containing constructs expressed in HEK293. [pal1991] Peptidyl-alpha-hydroxyglycine alpha-amidating lyase. Purification, characterization, and expression. (1991). https://pubmed.ncbi.nlm.nih.gov/1902227/ DOI: 10.1016/s0021-9258(20)89524-6

cross_nutrient

Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing.

experimental_model

Purified chick prolyl and partially purified lysyl collagen hydroxylases

exposure

Peptide substrate present or absent; uncoupled 2-oxoglutarate decarboxylation assays.

limitations

Substrate-free enzyme reaction; frequency and quantitative vitamin C cost of uncoupled cycles in human tissues were not measured.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Gallus gallus

plain_language

Vitamin C is consumed when this collagen enzyme runs a reaction cycle without hydroxylating its peptide target.

primary_references

[myllyla1984] Ascorbate is consumed stoichiometrically in the uncoupled reactions catalyzed by prolyl 4-hydroxylase and lysyl hydroxylase. (1984). https://pubmed.ncbi.nlm.nih.gov/6325436/ DOI: 10.1016/s0021-9258(18)91023-9

tissue_or_cell_type

Chick embryo enzyme preparations

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 598–609

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified chick prolyl and partially purified lysyl collagen hydroxylases · source_derived_draft · unverified_draft

### vc-enzyme-prolyl-uncoupled-consumption Chick collagen prolyl hydroxylase consumed ascorbate stoichiometrically during uncoupled 2-oxoglutarate decarboxylation in the absence of peptide substrate. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: Vitamin C is consumed when this collagen enzyme runs a reaction cycle without hydroxylating its peptide target. organism: Gallus gallus tissue_or_cell_type: Chick embryo enzyme preparations experimental_model: Purified chick prolyl and partially purified lysyl collagen hydroxylases limitations: Substrate-free enzyme reaction; frequency and quantitative vitamin C cost of uncoupled cycles in human tissues were not measured. cross_nutrient: Vitamin C chemistry in collagen, modified-lysine/carnitine metabolism or copper-dependent peptide/catecholamine processing. exposure: Peptide substrate present or absent; uncoupled 2-oxoglutarate decarboxylation assays. [myllyla1984] Ascorbate is consumed stoichiometrically in the uncoupled reactions catalyzed by prolyl 4-hydroxylase and lysyl hydroxylase. (1984). https://pubmed.ncbi.nlm.nih.gov/6325436/ DOI: 10.1016/s0021-9258(18)91023-9

cross_nutrient

Vitamin C + iron support hydroxylation of a modified lysine precursor; downstream existing SHMT steps use B6-derived PLP and ALDH9A1 uses NAD+.

experimental_model

Recombinant human MBP-TMLH-a; mass spectrometry and NMR

exposure

500 micromolar trimethyllysine and 3 micromolar enzyme, FeSO4/2OG/ascorbate, 37 C for 30 minutes; cofactor omission controls.

limitations

New record isolates the ascorbate cofactor dependence; the existing substrate-to-product UUID is reused. Fusion-protein assay does not quantify whole-body flux.

nutrient_topic

Vitamin C research collection; topical membership is not evidence of a direct dietary effect. · Vitamin C

organism

Homo sapiens

plain_language

The first carnitine-synthesis hydroxylation needs vitamin C support alongside iron and 2-oxoglutarate.

primary_references

[tmlh2016] Substrate scope for trimethyllysine hydroxylase catalysis. (2016). https://pubmed.ncbi.nlm.nih.gov/27730239/ DOI: 10.1039/c6cc07845a

tissue_or_cell_type

Cell-free recombinant enzyme

Vitamin C: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 689–700

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human MBP-TMLH-a; mass spectrometry and NMR · source_derived_draft · unverified_draft

### vc-enzyme-tmlh-ascorbate-dependency Omission controls with recombinant human MBP-TMLH-a showed that ascorbate, Fe(II) and 2-oxoglutarate were each needed for efficient conversion of free trimethyllysine to 3-hydroxytrimethyllysine. Condition category: normal nutrient_topic: Vitamin C research collection; topical membership is not evidence of a direct dietary effect. plain_language: The first carnitine-synthesis hydroxylation needs vitamin C support alongside iron and 2-oxoglutarate. organism: Homo sapiens tissue_or_cell_type: Cell-free recombinant enzyme experimental_model: Recombinant human MBP-TMLH-a; mass spectrometry and NMR limitations: New record isolates the ascorbate cofactor dependence; the existing substrate-to-product UUID is reused. Fusion-protein assay does not quantify whole-body flux. cross_nutrient: Vitamin C + iron support hydroxylation of a modified lysine precursor; downstream existing SHMT steps use B6-derived PLP and ALDH9A1 uses NAD+. exposure: 500 micromolar trimethyllysine and 3 micromolar enzyme, FeSO4/2OG/ascorbate, 37 C for 30 minutes; cofactor omission controls. [tmlh2016] Substrate scope for trimethyllysine hydroxylase catalysis. (2016). https://pubmed.ncbi.nlm.nih.gov/27730239/ DOI: 10.1039/c6cc07845a

evidence_span

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experimental_model

Purified human CDO1 crystallography, substrate binding, metal analysis and mutants

exposure

L-cysteine oxidation with molecular oxygen

limitations

The overall reaction and iron requirement are recorded; disputed detailed structural intermediates are not assigned as settled.

nutrient_topic

Molybdenum research collection; topical membership is not evidence of a direct dietary effect. · Molybdenum

organism

Homo sapiens

plain_language

Iron-dependent CDO1 starts an upstream sulfur-breakdown route.

primary_references

[mo-p17135237] An insight into the mechanism of human cysteine dioxygenase. Key roles of the thioether-bonded tyrosine-cysteine cofactor. (2007). https://pubmed.ncbi.nlm.nih.gov/17135237/ DOI: 10.1074/jbc.m609337200

tissue_or_cell_type

Recombinant human cysteine dioxygenase

Molybdenum: cofactor assembly, sulfur metabolism and nutrient interactions (2026-09-17) · lines 677–688

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human CDO1 crystallography, substrate binding, metal analysis and mutants · source_derived_draft · unverified_draft

### mo-cdo-csa Human CDO1 oxidizes cysteine to cysteine sulfinic acid using molecular oxygen and a non-heme iron center. Condition category: normal nutrient_topic: Molybdenum research collection; topical membership is not evidence of a direct dietary effect. plain_language: Iron-dependent CDO1 starts an upstream sulfur-breakdown route. organism: Homo sapiens tissue_or_cell_type: Recombinant human cysteine dioxygenase experimental_model: Purified human CDO1 crystallography, substrate binding, metal analysis and mutants limitations: The overall reaction and iron requirement are recorded; disputed detailed structural intermediates are not assigned as settled. exposure: L-cysteine oxidation with molecular oxygen evidence_span: {"source_cache": "artifacts/molybdenum-research/17135237.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "3ccd6f2de98887d17d935999238a88d8901fe8a66bb9b48c9cbd5d179bf180d6", "start_char": 0, "end_char": 1343, "text_sha256": "3ccd6f2de98887d17d935999238a88d8901fe8a66bb9b48c9cbd5d179bf180d6"} [mo-p17135237] An insight into the mechanism of human cysteine dioxygenase. Key roles of the thioether-bonded tyrosine-cysteine cofactor. (2007). https://pubmed.ncbi.nlm.nih.gov/17135237/ DOI: 10.1074/jbc.m609337200

evidence_span

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experimental_model

Recombinant human XDH variants with urate, superoxide and NO assays

exposure

Xanthine, oxygen and inorganic nitrite assays

limitations

The 2023 Fig. 6E corrigendum corrects a displayed panel; authors state data and conclusions are unchanged. Enzyme activity is not a clinical benefit or dietary response.

nutrient_topic

Molybdenum research collection; topical membership is not evidence of a direct dietary effect. · Molybdenum

organism

Homo sapiens protein

plain_language

The enzyme can generate oxidants as well as carry out purine breakdown.

primary_references

[mo-p37713777] Natural mutations of human XDH promote the nitrite (NO2-)-reductase capacity of xanthine oxidoreductase: A novel mechanism to promote redox health? (2023). https://pubmed.ncbi.nlm.nih.gov/37713777/ DOI: 10.1016/j.redox.2023.102864

tissue_or_cell_type

Purified human enzyme

Molybdenum: cofactor assembly, sulfur metabolism and nutrient interactions (2026-09-17) · lines 781–792

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human XDH variants with urate, superoxide and NO assays · source_derived_draft · unverified_draft

### mo-xor-oxygen In its oxidase activity, XOR can generate superoxide and hydrogen peroxide rather than exclusively transferring electrons to NAD+. Condition category: normal nutrient_topic: Molybdenum research collection; topical membership is not evidence of a direct dietary effect. plain_language: The enzyme can generate oxidants as well as carry out purine breakdown. organism: Homo sapiens protein tissue_or_cell_type: Purified human enzyme experimental_model: Recombinant human XDH variants with urate, superoxide and NO assays limitations: The 2023 Fig. 6E corrigendum corrects a displayed panel; authors state data and conclusions are unchanged. Enzyme activity is not a clinical benefit or dietary response. exposure: Xanthine, oxygen and inorganic nitrite assays evidence_span: {"source_cache": "artifacts/molybdenum-research/37713777.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "30e93ea24784120403bef1dfe72cf46411f1af88946b9cc1cba3d4c45a367bf9", "start_char": 0, "end_char": 1655, "text_sha256": "30e93ea24784120403bef1dfe72cf46411f1af88946b9cc1cba3d4c45a367bf9"} [mo-p37713777] Natural mutations of human XDH promote the nitrite (NO2-)-reductase capacity of xanthine oxidoreductase: A novel mechanism to promote redox health? (2023). https://pubmed.ncbi.nlm.nih.gov/37713777/ DOI: 10.1016/j.redox.2023.102864

evidence_location

Figure 3

experimental_model

Purified human BCO1 expressed in E. coli; substrate incubations and HPLC.

exposure

20 micromolar beta-carotene, 500 ng enzyme/200 microliters, 37 C, 15 minutes.

limitations

Purified-enzyme rates do not determine dietary conversion efficiency.

nutrient_topic

Vitamin A research collection; topical membership is not evidence of a direct dietary effect. · Vitamin A

organism

Homo sapiens protein expressed in Escherichia coli

outcome

Purified human BCO1 cleaved all-trans-beta-carotene centrally to all-trans-retinal.

plain_language

BCO1 turns a carotenoid precursor into retinal.

primary_references

[va-delasena-2013] Substrate specificity of purified recombinant human beta-carotene 15,15'-oxygenase (BCO1) (2013). https://pubmed.ncbi.nlm.nih.gov/24187135/ DOI: 10.1074/jbc.M113.507160

tissue_or_cell_type

Cell-free enzyme

Vitamin A: forms, mechanisms, deficiency and excess (2026-09-17) · lines 131–143

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human BCO1 expressed in E. coli; substrate incubations and HPLC. · source_derived_draft · unverified_draft

### va-bco1-central-cleavage Purified human BCO1 cleaved all-trans-beta-carotene centrally to all-trans-retinal. Condition category: normal nutrient_topic: Vitamin A research collection; topical membership is not evidence of a direct dietary effect. plain_language: BCO1 turns a carotenoid precursor into retinal. organism: Homo sapiens protein expressed in Escherichia coli tissue_or_cell_type: Cell-free enzyme experimental_model: Purified human BCO1 expressed in E. coli; substrate incubations and HPLC. limitations: Purified-enzyme rates do not determine dietary conversion efficiency. exposure: 20 micromolar beta-carotene, 500 ng enzyme/200 microliters, 37 C, 15 minutes. outcome: Purified human BCO1 cleaved all-trans-beta-carotene centrally to all-trans-retinal. evidence_location: Figure 3 [va-delasena-2013] Substrate specificity of purified recombinant human beta-carotene 15,15'-oxygenase (BCO1) (2013). https://pubmed.ncbi.nlm.nih.gov/24187135/ DOI: 10.1074/jbc.M113.507160

availability_state

nutrient_deficiency Imported condition classification; unverified.

evidence_span

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experimental_model

Protein association, ubiquitination and degradation experiments

exposure

Iron and oxygen availability; FBXL5 stability

limitations

Cellular sensing mechanism, not a serum-iron diagnostic rule.

nutrient_topic

Iron research collection; topical membership is not evidence of a direct dietary effect. · Iron

organism

Mammalian cellular systems

plain_language

The control system responds to both iron and oxygen availability.

primary_references

[iron-p19762596] Control of iron homeostasis by an iron-regulated ubiquitin ligase. (2009). https://pubmed.ncbi.nlm.nih.gov/19762596/ DOI: 10.1126/science.1176333

tissue_or_cell_type

Cytosolic iron regulation

trigger_kind

nutrient_deficiency Imported condition classification; unverified.

Iron: absorption, trafficking, iron-dependent enzymes and nutrient interactions (2026-09-17) · lines 693–704

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Protein association, ubiquitination and degradation experiments · source_derived_draft · unverified_draft

### iron-fbxl5-iron-sensing Iron or oxygen depletion triggered FBXL5 degradation through a process requiring its N-terminal hemerythrin-like iron-binding domain. Condition category: nutrient_deficiency nutrient_topic: Iron research collection; topical membership is not evidence of a direct dietary effect. plain_language: The control system responds to both iron and oxygen availability. organism: Mammalian cellular systems tissue_or_cell_type: Cytosolic iron regulation experimental_model: Protein association, ubiquitination and degradation experiments limitations: Cellular sensing mechanism, not a serum-iron diagnostic rule. exposure: Iron and oxygen availability; FBXL5 stability evidence_span: {"source_cache": "artifacts/iron-research/19762596.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "9308ac435b303ee150d6c92a21c3d68731fed61f0894312026a8a19e57d5aac6", "start_char": 0, "end_char": 824, "text_sha256": "9308ac435b303ee150d6c92a21c3d68731fed61f0894312026a8a19e57d5aac6"} [iron-p19762596] Control of iron homeostasis by an iron-regulated ubiquitin ligase. (2009). https://pubmed.ncbi.nlm.nih.gov/19762596/ DOI: 10.1126/science.1176333

evidence_span

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experimental_model

Ferroxidase kinetics and site-directed mutants

exposure

Fe(II) oxidation by oxygen; H-chain mutations and zinc inhibition

limitations

In-vitro metal concentrations and H/L composition determine kinetics; this does not establish a dietary zinc effect on human iron stores.

nutrient_topic

Iron research collection; topical membership is not evidence of a direct dietary effect. · Iron

organism

Human recombinant ferritin and human liver apoferritin

plain_language

Ferritin does chemical work to package iron, not just physical storage.

primary_references

[iron-p8369307] Ferroxidase kinetics of human liver apoferritin, recombinant H-chain apoferritin, and site-directed mutants. (1993). https://pubmed.ncbi.nlm.nih.gov/8369307/ DOI: 10.1021/bi00087a015

tissue_or_cell_type

Purified ferritin subunits/assemblies

Iron: absorption, trafficking, iron-dependent enzymes and nutrient interactions (2026-09-17) · lines 615–626

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Ferroxidase kinetics and site-directed mutants · source_derived_draft · unverified_draft

### iron-ferritin-h-oxidation Human H-chain ferritin catalyzed Fe(II) oxidation; mutation of its proposed ferroxidase ligands Glu62 and His65 abolished most activity. Condition category: normal nutrient_topic: Iron research collection; topical membership is not evidence of a direct dietary effect. plain_language: Ferritin does chemical work to package iron, not just physical storage. organism: Human recombinant ferritin and human liver apoferritin tissue_or_cell_type: Purified ferritin subunits/assemblies experimental_model: Ferroxidase kinetics and site-directed mutants limitations: In-vitro metal concentrations and H/L composition determine kinetics; this does not establish a dietary zinc effect on human iron stores. exposure: Fe(II) oxidation by oxygen; H-chain mutations and zinc inhibition evidence_span: {"source_cache": "artifacts/iron-research/8369307.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "8ccc94b97da4dcc2557e2f8ce964949b4188cd6c7e54405f6d4268ea864697ff", "start_char": 0, "end_char": 1709, "text_sha256": "8ccc94b97da4dcc2557e2f8ce964949b4188cd6c7e54405f6d4268ea864697ff"} [iron-p8369307] Ferroxidase kinetics of human liver apoferritin, recombinant H-chain apoferritin, and site-directed mutants. (1993). https://pubmed.ncbi.nlm.nih.gov/8369307/ DOI: 10.1021/bi00087a015

evidence_span

{"source_cache": "artifacts/iron-research/16765986.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "177ab81c08f82c99c81c69d1cb582e52216234e290066ae5aa380a887fb0e38c", "start_char": 0, "end_char": 1284, "text_sha256": "177ab81c08f82c99c81c69d1cb582e52216234e290066ae5aa380a887fb0e38c"}

experimental_model

High-resolution crystallographic comparison

exposure

1.25 angstrom structural refinement

limitations

Structural oxygen-ligand geometry, not a supplementation or oxygen-delivery clinical trial.

nutrient_topic

Iron research collection; topical membership is not evidence of a direct dietary effect. · Iron

organism

Human hemoglobin A

plain_language

Hemoglobin holds oxygen at carefully organized heme sites so oxygen binding can be controlled.

primary_references

[iron-p16765986] 1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. (2006). https://pubmed.ncbi.nlm.nih.gov/16765986/ DOI: 10.1016/j.jmb.2006.05.036

tissue_or_cell_type

Purified oxy-, deoxy- and carbonmonoxyhemoglobin

Iron: absorption, trafficking, iron-dependent enzymes and nutrient interactions (2026-09-17) · lines 537–548

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · High-resolution crystallographic comparison · source_derived_draft · unverified_draft

### iron-hemoglobin-oxygen-site Oxyhemoglobin structures resolved hydrogen bonding between the oxygen ligand and distal histidine in both alpha and beta subunits. Condition category: normal nutrient_topic: Iron research collection; topical membership is not evidence of a direct dietary effect. plain_language: Hemoglobin holds oxygen at carefully organized heme sites so oxygen binding can be controlled. organism: Human hemoglobin A tissue_or_cell_type: Purified oxy-, deoxy- and carbonmonoxyhemoglobin experimental_model: High-resolution crystallographic comparison limitations: Structural oxygen-ligand geometry, not a supplementation or oxygen-delivery clinical trial. exposure: 1.25 angstrom structural refinement evidence_span: {"source_cache": "artifacts/iron-research/16765986.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "177ab81c08f82c99c81c69d1cb582e52216234e290066ae5aa380a887fb0e38c", "start_char": 0, "end_char": 1284, "text_sha256": "177ab81c08f82c99c81c69d1cb582e52216234e290066ae5aa380a887fb0e38c"} [iron-p16765986] 1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. (2006). https://pubmed.ncbi.nlm.nih.gov/16765986/ DOI: 10.1016/j.jmb.2006.05.036

evidence_span

{"source_cache": "artifacts/inositol-research/18364358.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "9992644d489f26782d7ef0a70dc13ec5ca48e2b660a011173fba8e0d4e43ae19", "start_char": 0, "end_char": 1004, "text_sha256": "9992644d489f26782d7ef0a70dc13ec5ca48e2b660a011173fba8e0d4e43ae19"}

experimental_model

Human enzyme crystallography and catalytic analysis

exposure

Diiron center and inhibitor-bound structure

limitations

Catabolism of inositol is not evidence that humans synthesize vitamin C from it; the crystal ligand was an inhibitor.

nutrient_topic

Inositol research collection; topical membership is not evidence of a direct dietary effect. · Inositol (stereoisomer family)

organism

Homo sapiens

plain_language

MIOX opens the inositol ring, providing a route for its breakdown.

primary_references

[ino-p18364358] Structural and biophysical characterization of human myo-inositol oxygenase. (2008). https://pubmed.ncbi.nlm.nih.gov/18364358/ DOI: 10.1074/jbc.m800348200

tissue_or_cell_type

Purified MIOX

Inositol: synthesis, signaling, mineral interactions and conditional deficiency (2026-09-17) · lines 457–468

AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human enzyme crystallography and catalytic analysis · source_derived_draft · unverified_draft

### ino-miox-cleavage Human MIOX catalyzes oxidative cleavage of myo-inositol to D-glucuronate. Condition category: normal nutrient_topic: Inositol research collection; topical membership is not evidence of a direct dietary effect. plain_language: MIOX opens the inositol ring, providing a route for its breakdown. organism: Homo sapiens tissue_or_cell_type: Purified MIOX experimental_model: Human enzyme crystallography and catalytic analysis limitations: Catabolism of inositol is not evidence that humans synthesize vitamin C from it; the crystal ligand was an inhibitor. exposure: Diiron center and inhibitor-bound structure evidence_span: {"source_cache": "artifacts/inositol-research/18364358.abstract.txt", "locator": "Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "9992644d489f26782d7ef0a70dc13ec5ca48e2b660a011173fba8e0d4e43ae19", "start_char": 0, "end_char": 1004, "text_sha256": "9992644d489f26782d7ef0a70dc13ec5ca48e2b660a011173fba8e0d4e43ae19"} [ino-p18364358] Structural and biophysical characterization of human myo-inositol oxygenase. (2008). https://pubmed.ncbi.nlm.nih.gov/18364358/ DOI: 10.1074/jbc.m800348200

evidence_access

Primary abstract

experimental_model

Rat cerebellar NOS preparation; separated partial reactions.

limitations

Purified preparation; residual enzyme reductant supported a limited first reaction without added NADPH. This does not imply physiological NOS is NADPH independent.

nutrient_topic

L-Arginine collection; tissue, species, dose and formulation distinctions retained. · L-Arginine

plain_language

Nitric-oxide production passes through a distinct intermediate.

primary_references

Characteristics of the nitric oxide synthase-catalyzed conversion of arginine to N-hydroxyarginine, the first oxygenation step in the enzymic synthesis of nitric oxide. · 1995 · https://pubmed.ncbi.nlm.nih.gov/7530247/ · DOI 10.1074/jbc.270.4.1721

L-Arginine: transport, metabolic branches, nutrient interactions, availability and discovery questions (2026-09-18) · lines 70–76

AI-assisted research curation; primary-abstract references and experimental limitations individually identified. Not publisher full text. · supports · Rat cerebellar NOS preparation; separated partial reactions. · source_derived_draft · unverified_draft

## arg-nos-first Nitric-oxide production passes through a distinct intermediate. NOS converted arginine to N-hydroxyarginine in an oxygen- and calcium/calmodulin-dependent partial reaction. Model: Rat cerebellar NOS preparation; separated partial reactions. Limitations: Purified preparation; residual enzyme reductant supported a limited first reaction without added NADPH. This does not imply physiological NOS is NADPH independent. Evidence access: Primary abstract Characteristics of the nitric oxide synthase-catalyzed conversion of arginine to N-hydroxyarginine, the first oxygenation step in the enzymic synthesis of nitric oxide. · 1995 · https://pubmed.ncbi.nlm.nih.gov/7530247/ · DOI 10.1074/jbc.270.4.1721

evidence_access

Primary abstract

experimental_model

Rat cerebellar NOS preparation; separated partial reactions.

limitations

Purified preparation; residual enzyme reductant supported a limited first reaction without added NADPH. This does not imply physiological NOS is NADPH independent.

nutrient_topic

L-Arginine collection; tissue, species, dose and formulation distinctions retained. · L-Arginine

plain_language

The next reaction produces the signal and recycles the carbon skeleton.

primary_references

Characteristics of the nitric oxide synthase-catalyzed conversion of arginine to N-hydroxyarginine, the first oxygenation step in the enzymic synthesis of nitric oxide. · 1995 · https://pubmed.ncbi.nlm.nih.gov/7530247/ · DOI 10.1074/jbc.270.4.1721

L-Arginine: transport, metabolic branches, nutrient interactions, availability and discovery questions (2026-09-18) · lines 78–84

AI-assisted research curation; primary-abstract references and experimental limitations individually identified. Not publisher full text. · supports · Rat cerebellar NOS preparation; separated partial reactions. · source_derived_draft · unverified_draft

## arg-nos-second The next reaction produces the signal and recycles the carbon skeleton. The second oxygenation yielded NO and citrulline and required added NADPH and calcium/calmodulin. Model: Rat cerebellar NOS preparation; separated partial reactions. Limitations: Purified preparation; residual enzyme reductant supported a limited first reaction without added NADPH. This does not imply physiological NOS is NADPH independent. Evidence access: Primary abstract Characteristics of the nitric oxide synthase-catalyzed conversion of arginine to N-hydroxyarginine, the first oxygenation step in the enzymic synthesis of nitric oxide. · 1995 · https://pubmed.ncbi.nlm.nih.gov/7530247/ · DOI 10.1074/jbc.270.4.1721