Component

Ammonia

Independent small molecule record; interpretation is limited by each linked claim and its study context.

15 recorded relationships. Experimental role, claim status and evidence remain attached to each record.

Read recorded mechanisms Open recursive mind map

How nutrients influence it

Every nutrient with a recorded effect on this component, credited to the nutrient that acted rather than the chapter that recorded it. Open a nutrient to see the findings and the conditions they were measured under.

How nutrients reach it in more than one step

Chains of two or more recorded steps that end here, grouped by the nutrient they start from. Each step is a separate finding, so a chain is a route a mechanism could take, not proof that it does.

Tracing routes…

What it does

Every recorded relationship this component is part of, grouped by its role. Plain wording comes first; the technical statement follows.

Recorded relationships

Where it participates (unsigned role)

  1. Human AMT transfers the aminomethyl-lipoyl intermediate's carbon to tetrahydrofolate, yielding 5,10-methylene-THF, ammonia and reduced H-protein.

    Human aminomethyltransferase / glycine-cleavage T-protein → 5,10-Methylenetetrahydrofolate source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    B6-dependent GLDC precedes lipoyl-carrier transfer and folate-dependent AMT chemistry.
    experimental_model
    Purified human AMT structures and mutational analyses
    limitations
    AMT is the directly examined human enzyme; this study did not test dietary B6 depletion or the entire pathway flux.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Glycine cleavage connects its B6-dependent first step to a separate folate-dependent step.
    primary_references
    [b6-amt-2005] Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia. (2005). https://pubmed.ncbi.nlm.nih.gov/16051266/ DOI: 10.1016/j.jmb.2005.06.056
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 682–692

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human AMT structures and mutational analyses · source_derived_draft · unverified_draft

    ### b6-met-amt-onecarbon Human AMT transfers the aminomethyl-lipoyl intermediate's carbon to tetrahydrofolate, yielding 5,10-methylene-THF, ammonia and reduced H-protein. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Glycine cleavage connects its B6-dependent first step to a separate folate-dependent step. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified human AMT structures and mutational analyses limitations: AMT is the directly examined human enzyme; this study did not test dietary B6 depletion or the entire pathway flux. cross_nutrient: B6-dependent GLDC precedes lipoyl-carrier transfer and folate-dependent AMT chemistry. [b6-amt-2005] Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia. (2005). https://pubmed.ncbi.nlm.nih.gov/16051266/ DOI: 10.1016/j.jmb.2005.06.056
    Complete structured claim and evidence

  2. Human CTH cleaves cystathionine to cysteine, 2-oxobutanoate and ammonia in a PLP-dependent reaction.

    Human cystathionine gamma-lyase / CTH → Cystathionine source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    B6-dependent sulfur transfer supplies cysteine; glutathione synthesis requires additional enzymes.
    experimental_model
    Purified human CTH apo/holo crystal structures and assays
    limitations
    Purified-enzyme evidence does not define dietary requirements or cellular PLP thresholds.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    This step releases cysteine for downstream metabolism.
    primary_references
    [b6-cth-structure-2009] Structural Basis for the Inhibition Mechanism of Human Cystathionine gamma-Lyase, an Enzyme Responsible for the Production of H2S (2009). https://doi.org/10.1074/jbc.M805459200 DOI: 10.1074/jbc.M805459200
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 554–564

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human CTH apo/holo crystal structures and assays · source_derived_draft · unverified_draft

    ### b6-met-cth-cleavage Human CTH cleaves cystathionine to cysteine, 2-oxobutanoate and ammonia in a PLP-dependent reaction. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: This step releases cysteine for downstream metabolism. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified human CTH apo/holo crystal structures and assays limitations: Purified-enzyme evidence does not define dietary requirements or cellular PLP thresholds. cross_nutrient: B6-dependent sulfur transfer supplies cysteine; glutathione synthesis requires additional enzymes. [b6-cth-structure-2009] Structural Basis for the Inhibition Mechanism of Human Cystathionine gamma-Lyase, an Enzyme Responsible for the Production of H2S (2009). https://doi.org/10.1074/jbc.M805459200 DOI: 10.1074/jbc.M805459200
    Complete structured claim and evidence

  3. Renal mitochondria from potassium-depleted rats produced more ammonia during glutamine-metabolism assays after three days of potassium-free feeding.

    Potassium → Renal ammonia production source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    nutrient_deficiency Imported condition classification; unverified.
    cross_nutrient
    Potassium depletion changes mitochondrial glutamine nitrogen metabolism; enzyme capacity and substrate entry need separate accounting.
    endpoint
    Renal mitochondria from potassium-depleted rats produced more ammonia during glutamine-metabolism assays after three days of potassium-free feeding.
    experimental-exposure
    Rats on potassium-free diet with renal mitochondrial and cortical-tubule ammonia assays during depletion and potassium refeeding.
    experimental_model
    Rats on potassium-free diet with renal mitochondrial and cortical-tubule ammonia assays during depletion and potassium refeeding.
    limitations
    Isolated mitochondrial assay, not whole-body bicarbonate balance. Glutaminase activity rose earlier than ammonia flux; mitochondrial glutamine entry was proposed as a limiting step.
    nutrient_topic
    Potassium research collection; topical membership is not evidence of a direct dietary effect. · Potassium
    organism
    Rattus norvegicus
    plain_language
    The kidney adaptation included greater ammonia production, beyond changes in enzyme abundance.
    primary_references
    [sastrasinh-1986-mitochondrial-ammonia] Renal mitochondrial glutamine metabolism during K+ depletion (1986). https://pubmed.ncbi.nlm.nih.gov/3963205/ DOI: 10.1152/ajprenal.1986.250.4.F667
    tissue_or_cell_type
    renal mitochondria
    trigger_kind
    nutrient_deficiency Imported condition classification; unverified.

    Potassium: cross-nutrient mechanisms and deficiency (2026-09-17) · lines 1041–1053

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Rats on potassium-free diet with renal mitochondrial and cortical-tubule ammonia assays during depletion and potassium refeeding. · source_derived_draft · unverified_draft

    ### k-depletion-increases-mitochondrial-ammonia Renal mitochondria from potassium-depleted rats produced more ammonia during glutamine-metabolism assays after three days of potassium-free feeding. Condition category: nutrient_deficiency nutrient_topic: Potassium research collection; topical membership is not evidence of a direct dietary effect. plain_language: The kidney adaptation included greater ammonia production, beyond changes in enzyme abundance. organism: Rattus norvegicus tissue_or_cell_type: renal mitochondria experimental_model: Rats on potassium-free diet with renal mitochondrial and cortical-tubule ammonia assays during depletion and potassium refeeding. limitations: Isolated mitochondrial assay, not whole-body bicarbonate balance. Glutaminase activity rose earlier than ammonia flux; mitochondrial glutamine entry was proposed as a limiting step. cross_nutrient: Potassium depletion changes mitochondrial glutamine nitrogen metabolism; enzyme capacity and substrate entry need separate accounting. experimental-exposure: Rats on potassium-free diet with renal mitochondrial and cortical-tubule ammonia assays during depletion and potassium refeeding. endpoint: Renal mitochondria from potassium-depleted rats produced more ammonia during glutamine-metabolism assays after three days of potassium-free feeding. [sastrasinh-1986-mitochondrial-ammonia] Renal mitochondrial glutamine metabolism during K+ depletion (1986). https://pubmed.ncbi.nlm.nih.gov/3963205/ DOI: 10.1152/ajprenal.1986.250.4.F667
    Complete structured claim and evidence

  4. NBCe1-A deletion blunted the urinary ammonia-excretion response to potassium-free feeding.

    NBCe1-A splice variant → Urinary total ammonia excretion source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    cross_nutrient
    Sodium-bicarbonate transport machinery is required for the full potassium-responsive ammonia adaptation.
    endpoint
    NBCe1-A deletion blunted the urinary ammonia-excretion response to potassium-free feeding.
    experimental-exposure
    NBCe1-A-selective knockout mice and wild-type littermates on control or potassium-free diets; four-day response.
    experimental_model
    NBCe1-A-selective knockout mice and wild-type littermates on control or potassium-free diets; four-day response.
    limitations
    Assay reports total ammonia. Knockout also causes acidosis and outer-medullary compensation; the exact signal is unresolved.
    nutrient_topic
    Potassium research collection; topical membership is not evidence of a direct dietary effect. · Potassium
    organism
    Mus musculus
    plain_language
    A sodium-bicarbonate transporter was needed for the full kidney ammonia response to potassium deprivation.
    primary_references
    [lee-2020-nbce1a] NBCe1-A is required for the renal ammonia and K+ response to hypokalemia (2020). https://pubmed.ncbi.nlm.nih.gov/31841393/ DOI: 10.1152/ajprenal.00481.2019
    tissue_or_cell_type
    cortical proximal tubule and urinary ammonia output
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Potassium: cross-nutrient mechanisms and deficiency (2026-09-17) · lines 1082–1094

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · NBCe1-A-selective knockout mice and wild-type littermates on control or potassium-free diets; four-day response. · source_derived_draft · unverified_draft

    ### nbce1a-loss-blunts-k-ammonia-response NBCe1-A deletion blunted the urinary ammonia-excretion response to potassium-free feeding. Condition category: machinery_impairment nutrient_topic: Potassium research collection; topical membership is not evidence of a direct dietary effect. plain_language: A sodium-bicarbonate transporter was needed for the full kidney ammonia response to potassium deprivation. organism: Mus musculus tissue_or_cell_type: cortical proximal tubule and urinary ammonia output experimental_model: NBCe1-A-selective knockout mice and wild-type littermates on control or potassium-free diets; four-day response. limitations: Assay reports total ammonia. Knockout also causes acidosis and outer-medullary compensation; the exact signal is unresolved. cross_nutrient: Sodium-bicarbonate transport machinery is required for the full potassium-responsive ammonia adaptation. experimental-exposure: NBCe1-A-selective knockout mice and wild-type littermates on control or potassium-free diets; four-day response. endpoint: NBCe1-A deletion blunted the urinary ammonia-excretion response to potassium-free feeding. [lee-2020-nbce1a] NBCe1-A is required for the renal ammonia and K+ response to hypokalemia (2020). https://pubmed.ncbi.nlm.nih.gov/31841393/ DOI: 10.1152/ajprenal.00481.2019
    Complete structured claim and evidence

  5. LC-MS analysis supported amination of 3,4,5-Trihydroxyphenylacetic acid in myricetin-treated mice.

    3,4,5-Trihydroxyphenylacetic acid → Aminated 3,4,5-trihydroxyphenylacetic acid; positional assignment unresolved source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary abstract
    experimental_model
    Mouse fecal/plasma metabolite analysis after oral dosing.
    limitations
    Structural certainty differs from the NMR-confirmed parent amination product; no human flux measured.
    nutrient_topic
    Myricetin collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Myricetin
    plain_language
    Downstream products can undergo further chemistry.
    primary_references
    Biotransformation of Myricetin: A Novel Metabolic Pathway to Produce Aminated Products in Mice. · 2019 · https://pubmed.ncbi.nlm.nih.gov/31087612/ · DOI 10.1002/mnfr.201900203

    Myricetin: metabolism, immune signaling, redox chemistry and cross-nutrient mechanisms (2026-09-19) · lines 92–98

    AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Mouse fecal/plasma metabolite analysis after oral dosing. · source_derived_draft · unverified_draft

    ## myricetin-acid-amination Downstream products can undergo further chemistry. LC-MS analysis supported amination of 3,4,5-Trihydroxyphenylacetic acid in myricetin-treated mice. Model: Mouse fecal/plasma metabolite analysis after oral dosing. Limitations: Structural certainty differs from the NMR-confirmed parent amination product; no human flux measured. Evidence access: Primary abstract Biotransformation of Myricetin: A Novel Metabolic Pathway to Produce Aminated Products in Mice. · 2019 · https://pubmed.ncbi.nlm.nih.gov/31087612/ · DOI 10.1002/mnfr.201900203
    Complete structured claim and evidence

  6. Oxidized myricetin reacted chemically with ammonia to form 4′-NH2-myricetin, structurally confirmed by NMR and LC-MS.

    Myricetin quinone, oxidation intermediate → 4′-NH2-myricetin source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary abstract
    experimental_model
    Cell-free chemistry.
    limitations
    Not an established ammonia-detoxification therapy or enzyme-catalyzed pathway.
    nutrient_topic
    Myricetin collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Myricetin
    plain_language
    Reactive nitrogen can become part of a new metabolite.
    primary_references
    Biotransformation of Myricetin: A Novel Metabolic Pathway to Produce Aminated Products in Mice. · 2019 · https://pubmed.ncbi.nlm.nih.gov/31087612/ · DOI 10.1002/mnfr.201900203

    Myricetin: metabolism, immune signaling, redox chemistry and cross-nutrient mechanisms (2026-09-19) · lines 44–50

    AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Cell-free chemistry. · source_derived_draft · unverified_draft

    ## myricetin-amination-chemistry Reactive nitrogen can become part of a new metabolite. Oxidized myricetin reacted chemically with ammonia to form 4′-NH2-myricetin, structurally confirmed by NMR and LC-MS. Model: Cell-free chemistry. Limitations: Not an established ammonia-detoxification therapy or enzyme-catalyzed pathway. Evidence access: Primary abstract Biotransformation of Myricetin: A Novel Metabolic Pathway to Produce Aminated Products in Mice. · 2019 · https://pubmed.ncbi.nlm.nih.gov/31087612/ · DOI 10.1002/mnfr.201900203
    Complete structured claim and evidence

  7. LC-MS analysis supported amination of Mono-O-methylated myricetin; positional isomer unresolved in myricetin-treated mice.

    Mono-O-methylated myricetin; positional isomer unresolved → Aminated mono-O-methylated myricetin; positional isomer unresolved source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary abstract
    experimental_model
    Mouse fecal/plasma metabolite analysis after oral dosing.
    limitations
    Structural certainty differs from the NMR-confirmed parent amination product; no human flux measured.
    nutrient_topic
    Myricetin collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Myricetin
    plain_language
    Downstream products can undergo further chemistry.
    primary_references
    Biotransformation of Myricetin: A Novel Metabolic Pathway to Produce Aminated Products in Mice. · 2019 · https://pubmed.ncbi.nlm.nih.gov/31087612/ · DOI 10.1002/mnfr.201900203

    Myricetin: metabolism, immune signaling, redox chemistry and cross-nutrient mechanisms (2026-09-19) · lines 84–90

    AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Mouse fecal/plasma metabolite analysis after oral dosing. · source_derived_draft · unverified_draft

    ## myricetin-methyl-amination Downstream products can undergo further chemistry. LC-MS analysis supported amination of Mono-O-methylated myricetin; positional isomer unresolved in myricetin-treated mice. Model: Mouse fecal/plasma metabolite analysis after oral dosing. Limitations: Structural certainty differs from the NMR-confirmed parent amination product; no human flux measured. Evidence access: Primary abstract Biotransformation of Myricetin: A Novel Metabolic Pathway to Produce Aminated Products in Mice. · 2019 · https://pubmed.ncbi.nlm.nih.gov/31087612/ · DOI 10.1002/mnfr.201900203
    Complete structured claim and evidence

  8. Purified human hepatic serine dehydratase showed L-threonine dehydratase activity in comparison with the human SDH-like isoform.

    Human hepatic serine dehydratase / SDS → Alpha-ketobutyrate source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary abstract
    experimental_model
    Human recombinant enzymes expressed in E. coli and compared biochemically.
    limitations
    Activity in a purified system does not quantify whole-body human threonine flux. The threonine product is alpha-ketobutyrate, distinct from the serine product pyruvate.
    nutrient_topic
    L-Threonine collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Threonine
    plain_language
    Threonine can enter carbon metabolism through an enzyme it shares with serine.
    primary_references
    Enzymatic and biochemical properties of a novel human serine dehydratase isoform. · 2006 · https://pubmed.ncbi.nlm.nih.gov/16580895/ · DOI 10.1016/j.bbapap.2006.02.010

    L-Threonine: translation, intestinal barrier, metabolism and cross-nutrient mechanisms (2026-09-19) · lines 250–256

    AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Human recombinant enzymes expressed in E. coli and compared biochemically. · source_derived_draft · unverified_draft

    ## l-threonine-human-sds-catabolism Threonine can enter carbon metabolism through an enzyme it shares with serine. Purified human hepatic serine dehydratase showed L-threonine dehydratase activity in comparison with the human SDH-like isoform. Model: Human recombinant enzymes expressed in E. coli and compared biochemically. Limitations: Activity in a purified system does not quantify whole-body human threonine flux. The threonine product is alpha-ketobutyrate, distinct from the serine product pyruvate. Evidence access: Primary abstract Enzymatic and biochemical properties of a novel human serine dehydratase isoform. · 2006 · https://pubmed.ncbi.nlm.nih.gov/16580895/ · DOI 10.1016/j.bbapap.2006.02.010
    Complete structured claim and evidence

  9. CPS1 uses two ATP-dependent phosphorylation steps to convert bicarbonate and ammonia into carbamoyl phosphate.

    Human carbamoyl-phosphate synthetase 1 / CPS1 → Carbamoyl phosphate source_derived_draftungraded
    Experimental context and source evidence
    evidence_span
    {"source_cache": "artifacts/citrulline-research/26592762.fulltext.txt", "locator": "Primary full-text span; zero-based, end-exclusive Unicode character offsets", "file_sha256": "9807338d87ba1b5602512aa3765c7cc48d391595cc1f35e6a43bcbe1250d3c7d", "start_char": 1169, "end_char": 1477, "text_sha256": "c5e2a8e1d3e3a09064b7b233635f7d573f8761b3f6ae18a68bc9b102a2d5874c"}
    experimental_model
    Human recombinant enzyme crystallography and mutation analysis
    exposure
    Structures without NAG and with NAG plus nucleotides
    limitations
    Mechanism of enzyme activation; clinical effects of adding nutritional cofactors were not tested.
    nutrient_topic
    Citrulline research collection; topical membership is not evidence of a direct dietary effect. · L-Citrulline
    organism
    Human CPS1
    plain_language
    The upstream part of citrulline synthesis consumes energy to handle ammonia.
    primary_references
    [citrulline-p26592762] Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis. (2015). https://pubmed.ncbi.nlm.nih.gov/26592762/ DOI: 10.1038/srep16950
    tissue_or_cell_type
    Mitochondrial carbamoyl-phosphate synthesis

    Citrulline: arginine recycling, nitrogen disposal and nutrient connections (2026-09-17) · lines 242–253

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

    ### citrulline-cps1-product CPS1 uses two ATP-dependent phosphorylation steps to convert bicarbonate and ammonia into carbamoyl phosphate. Condition category: normal nutrient_topic: Citrulline research collection; topical membership is not evidence of a direct dietary effect. plain_language: The upstream part of citrulline synthesis consumes energy to handle ammonia. organism: Human CPS1 tissue_or_cell_type: Mitochondrial carbamoyl-phosphate synthesis experimental_model: Human recombinant enzyme crystallography and mutation analysis limitations: Mechanism of enzyme activation; clinical effects of adding nutritional cofactors were not tested. exposure: Structures without NAG and with NAG plus nucleotides evidence_span: {"source_cache": "artifacts/citrulline-research/26592762.fulltext.txt", "locator": "Primary full-text span; zero-based, end-exclusive Unicode character offsets", "file_sha256": "9807338d87ba1b5602512aa3765c7cc48d391595cc1f35e6a43bcbe1250d3c7d", "start_char": 1169, "end_char": 1477, "text_sha256": "c5e2a8e1d3e3a09064b7b233635f7d573f8761b3f6ae18a68bc9b102a2d5874c"} [citrulline-p26592762] Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis. (2015). https://pubmed.ncbi.nlm.nih.gov/26592762/ DOI: 10.1038/srep16950
    Complete structured claim and evidence

  10. Purified human NADSYN1 also supported NAD+ formation with free ammonia; its reported catalytic efficiencies for glutamine and ammonia were similar, 0.45 and 0.49 per second per millimolar.

    Human glutamine-dependent NAD synthetase / NADSYN1 → NAD+ source_derived_draftungraded
    Experimental context and source evidence
    evidence_span
    {"source_cache": "artifacts/niacin-precursors-sources/nadsyn2019.paragraphs.txt", "locator": "Normalized full-text paragraphs 8–8 (0-based)", "start_char": 7090, "end_char": 8684, "file_sha256": "36ad82ce734c8e0c44d01c7dc813b1641708738319b53a926e429155b1a602f4", "text_sha256": "90cb4d2ce3001f2ecf18f1d751db36047726b71a75be94b073474f6f518c96cd"}
    experimental_model
    Recombinant human NADSYN1 steady-state kinetic assays and crystallography; bacterial comparison kept separate
    exposure
    Biochemical or structural assay; no dietary intervention
    limitations
    Assay substrate efficiency does not show that free ammonia replaces glutamine physiologically or justify ammonia exposure.
    nutrient_topic
    Niacin research collection; topical membership is not evidence of a direct dietary effect. · Niacin (vitamin B3)
    organism
    Homo sapiens
    plain_language
    Human NADSYN1 can use either tested nitrogen source in vitro.
    primary_references
    [b3-pre-nadsyn2019] Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+ synthetases. (2020). https://pubmed.ncbi.nlm.nih.gov/31911602/ DOI: 10.1038/s41467-019-13845-4
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Niacin: NAD metabolism, deficiency and nutrient interactions (2026-09-17) · lines 356–367

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human NADSYN1 steady-state kinetic assays and crystallography; bacterial comparison kept separate · source_derived_draft · unverified_draft

    ### b3-pre-nadsyn-ammonia Purified human NADSYN1 also supported NAD+ formation with free ammonia; its reported catalytic efficiencies for glutamine and ammonia were similar, 0.45 and 0.49 per second per millimolar. Condition category: normal nutrient_topic: Niacin research collection; topical membership is not evidence of a direct dietary effect. plain_language: Human NADSYN1 can use either tested nitrogen source in vitro. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Recombinant human NADSYN1 steady-state kinetic assays and crystallography; bacterial comparison kept separate limitations: Assay substrate efficiency does not show that free ammonia replaces glutamine physiologically or justify ammonia exposure. exposure: Biochemical or structural assay; no dietary intervention evidence_span: {"source_cache": "artifacts/niacin-precursors-sources/nadsyn2019.paragraphs.txt", "locator": "Normalized full-text paragraphs 8–8 (0-based)", "start_char": 7090, "end_char": 8684, "file_sha256": "36ad82ce734c8e0c44d01c7dc813b1641708738319b53a926e429155b1a602f4", "text_sha256": "90cb4d2ce3001f2ecf18f1d751db36047726b71a75be94b073474f6f518c96cd"} [b3-pre-nadsyn2019] Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+ synthetases. (2020). https://pubmed.ncbi.nlm.nih.gov/31911602/ DOI: 10.1038/s41467-019-13845-4
    Complete structured claim and evidence

  11. Human glutamine synthetase catalyzes ATP-coupled ligation of glutamate and ammonia to make glutamine.

    Glutamine synthetase / GLUL → L-Glutamine source_derived_draftungraded
    Experimental context and source evidence
    experimental_model
    Human GLUL ligand-complex crystal structures; canine apoenzyme comparison
    exposure
    ADP/phosphate/Mn and ADP/phosphorylated-inhibitor/Mn complexes
    limitations
    Reaction identity does not determine the predominant metal in living human brain.
    nutrient_topic
    Manganese research collection; topical membership is not evidence of a direct dietary effect. · Manganese
    organism
    Homo sapiens protein
    plain_language
    GLUL combines glutamate and ammonia using ATP.
    primary_references
    [mn-enz-18005987] Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design. (2008). https://pubmed.ncbi.nlm.nih.gov/18005987/ DOI: 10.1016/j.jmb.2007.10.029
    tissue_or_cell_type
    Purified GLUL

    Manganese: enzyme cofactors, glycosylation, transport and nutrient interactions (2026-09-17) · lines 596–606

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human GLUL ligand-complex crystal structures; canine apoenzyme comparison · source_derived_draft · unverified_draft

    ### mn-enz-glul-reaction Human glutamine synthetase catalyzes ATP-coupled ligation of glutamate and ammonia to make glutamine. Condition category: normal nutrient_topic: Manganese research collection; topical membership is not evidence of a direct dietary effect. plain_language: GLUL combines glutamate and ammonia using ATP. organism: Homo sapiens protein tissue_or_cell_type: Purified GLUL experimental_model: Human GLUL ligand-complex crystal structures; canine apoenzyme comparison limitations: Reaction identity does not determine the predominant metal in living human brain. exposure: ADP/phosphate/Mn and ADP/phosphorylated-inhibitor/Mn complexes [mn-enz-18005987] Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design. (2008). https://pubmed.ncbi.nlm.nih.gov/18005987/ DOI: 10.1016/j.jmb.2007.10.029
    Complete structured claim and evidence

  12. Lysyl-oxidase activity can convert collagen hydroxylysine side chains to hydroxyallysine.

    Lysyl oxidase enzyme family → Collagen-bound 5-hydroxylysine residues source_derived_draftungraded
    Experimental context and source evidence
    experimental_model
    LOXL2 assay development with extracellular matrix; family-level reaction context.
    limitations
    This is a reaction-class record; not every hydroxylysine site is an accessible LOX substrate.
    organism
    Mammalian cells/tissues and recombinant LOXL2; see study methods
    plain_language
    Hydroxylated lysines provide a different aldehyde starting point for cross-links.
    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 477–485

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · LOXL2 assay development with extracellular matrix; family-level reaction context. · source_derived_draft · unverified_draft

    ### lox-hydroxylysine-oxidation Lysyl-oxidase activity can convert collagen hydroxylysine side chains to hydroxyallysine. Plain language: Hydroxylated lysines provide a different aldehyde starting point for cross-links. 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 with extracellular matrix; family-level reaction context. limitations: This is a reaction-class record; not every hydroxylysine site is an accessible LOX substrate. [lox-assay-2021] An in situ activity assay for lysyl oxidases (2021). https://pubmed.ncbi.nlm.nih.gov/34226627/
    Complete structured claim and evidence

  13. Lysyl oxidase converts suitable peptidyl lysines to allysine, producing ammonia and hydrogen peroxide.

    Lysyl oxidase enzyme family → Collagen/elastin peptidyl lysine substrates source_derived_draftungraded
    Experimental context and source evidence
    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/
    Complete structured claim and evidence

  14. Got1 deficiency lowered 2-oxoglutarate production from glutamine metabolism and caused toxic ammonia accumulation in mouse CD8 T cells during chronic infection.

    T-cell-specific Got1 loss in mice → Ammonia accumulation in Got1-deficient mouse T cells source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    evidence_access
    Primary abstract
    experimental_model
    Mouse T-cell-specific gene deletion and chronic LCMV infection.
    limitations
    This is a cell-state-specific mechanism, not a universal definition of malate–aspartate shuttle function.
    nutrient_topic
    L-Aspartate collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Aspartate
    plain_language
    The transaminase also helped manage the nitrogen released while using glutamine.
    primary_references
    The malate shuttle detoxifies ammonia in exhausted T cells by producing 2-ketoglutarate. · 2023 · https://pubmed.ncbi.nlm.nih.gov/37813964/ · DOI 10.1038/s41590-023-01636-5
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    L-Aspartate: redox transfer, nitrogen partitioning and cross-nutrient mechanisms (2026-09-19) · lines 298–304

    AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Mouse T-cell-specific gene deletion and chronic LCMV infection. · source_derived_draft · unverified_draft

    ## l-aspartate-tcell-ammonia The transaminase also helped manage the nitrogen released while using glutamine. Got1 deficiency lowered 2-oxoglutarate production from glutamine metabolism and caused toxic ammonia accumulation in mouse CD8 T cells during chronic infection. Model: Mouse T-cell-specific gene deletion and chronic LCMV infection. Limitations: This is a cell-state-specific mechanism, not a universal definition of malate–aspartate shuttle function. Evidence access: Primary abstract The malate shuttle detoxifies ammonia in exhausted T cells by producing 2-ketoglutarate. · 2023 · https://pubmed.ncbi.nlm.nih.gov/37813964/ · DOI 10.1038/s41590-023-01636-5
    Complete structured claim and evidence

  15. Rat FTCD cyclodeaminase converts 5-formimino-THF to 5,10-methenyl-THF with ammonia release.

    Rat formiminotransferase cyclodeaminase / FTCD → 5-Formiminotetrahydrofolate source_derived_draftungraded
    Experimental context and source evidence
    evidence_location
    Cyclodeaminase active-site results and enzyme assay methods.
    experimental_model
    Recombinant protein catalytic assay and mutagenesis
    exposure
    Recombinant rat FTCD and CD-site mutants.
    limitations
    Rat enzyme; human catalytic rates are not measured.
    nutrient_topic
    Folate and folic acid research collection; topical membership is not evidence of a direct dietary effect. · Folate (vitamin B9)
    organism
    Rattus norvegicus
    plain_language
    A second enzyme domain converts the transferred group into methenyl-folate.
    primary_references
    [mao-2004] Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer (2004). https://pubmed.ncbi.nlm.nih.gov/15272307/ DOI: 10.1038/sj.emboj.7600327
    tissue_or_cell_type
    Cell-free

    Folate and folic acid: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1308–1319

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant protein catalytic assay and mutagenesis · source_derived_draft · unverified_draft

    ### rat-ftcd-cyclodeamination Rat FTCD cyclodeaminase converts 5-formimino-THF to 5,10-methenyl-THF with ammonia release. Condition category: normal nutrient_topic: Folate and folic acid research collection; topical membership is not evidence of a direct dietary effect. plain_language: A second enzyme domain converts the transferred group into methenyl-folate. organism: Rattus norvegicus tissue_or_cell_type: Cell-free experimental_model: Recombinant protein catalytic assay and mutagenesis limitations: Rat enzyme; human catalytic rates are not measured. exposure: Recombinant rat FTCD and CD-site mutants. evidence_location: Cyclodeaminase active-site results and enzyme assay methods. [mao-2004] Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer (2004). https://pubmed.ncbi.nlm.nih.gov/15272307/ DOI: 10.1038/sj.emboj.7600327
    Complete structured claim and evidence

In the sources

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