Component

Pyridoxamine 5-prime-phosphate

Phosphorylated pyridoxamine, a PNPO substrate.

9 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

What acts on it

  1. Pre-steady-state analysis of human AGXT showed that PMP remained bound during its catalytic cycle and the AGXT–PMP complex reacted efficiently with oxo-acid substrates.

    Human peroxisomal alanine:glyoxylate aminotransferase / AGXT → Pyridoxamine 5-prime-phosphate source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary abstract
    experimental_model
    Purified human AGXT; PLP-form reactions with alanine/glycine and PMP-form reactions with pyruvate/glyoxylate.
    limitations
    Cofactor cycling is not evidence that B6 is irreversibly consumed once per reaction.
    nutrient_topic
    L-Alanine collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Alanine
    plain_language
    The B6 cofactor changes form while helping transfer nitrogen.
    primary_references
    Human wild-type alanine:glyoxylate aminotransferase and its naturally occurring G82E variant: functional properties and physiological implications. · 2007 · https://pubmed.ncbi.nlm.nih.gov/17696873/ · DOI 10.1042/BJ20070637

    L-Alanine: carbon, nitrogen, protein synthesis and cross-nutrient mechanisms (2026-09-19) · lines 40–46

    AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Purified human AGXT; PLP-form reactions with alanine/glycine and PMP-form reactions with pyruvate/glyoxylate. · source_derived_draft · unverified_draft

    ## alanine-agt-pmp-cycle The B6 cofactor changes form while helping transfer nitrogen. Pre-steady-state analysis of human AGXT showed that PMP remained bound during its catalytic cycle and the AGXT–PMP complex reacted efficiently with oxo-acid substrates. Model: Purified human AGXT; PLP-form reactions with alanine/glycine and PMP-form reactions with pyruvate/glyoxylate. Limitations: Cofactor cycling is not evidence that B6 is irreversibly consumed once per reaction. Evidence access: Primary abstract Human wild-type alanine:glyoxylate aminotransferase and its naturally occurring G82E variant: functional properties and physiological implications. · 2007 · https://pubmed.ncbi.nlm.nih.gov/17696873/ · DOI 10.1042/BJ20070637
    Complete structured claim and evidence

  2. Human BCAT2 structures capture the isoleucine ketimine and PMP forms of its amino-transfer cycle.

    Human mitochondrial branched-chain aminotransferase / BCAT2 → Pyridoxamine 5-prime-phosphate source_derived_draftungraded
    Experimental context and source evidence
    experimental_model
    Human BCAT2 reaction-intermediate crystallography
    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
    The cofactor cycles between PLP and PMP as it carries an amino group.
    primary_references
    [b6-bcat2-2002] Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms (2002). https://pubmed.ncbi.nlm.nih.gov/12269802/ DOI: 10.1021/bi020221c
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 706–715

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human BCAT2 reaction-intermediate crystallography · source_derived_draft · unverified_draft

    ### b6-met-bcat2-pmp Human BCAT2 structures capture the isoleucine ketimine and PMP forms of its amino-transfer cycle. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: The cofactor cycles between PLP and PMP as it carries an amino group. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Human BCAT2 reaction-intermediate crystallography limitations: Purified-enzyme evidence does not define dietary requirements or cellular PLP thresholds. [b6-bcat2-2002] Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms (2002). https://pubmed.ncbi.nlm.nih.gov/12269802/ DOI: 10.1021/bi020221c
    Complete structured claim and evidence

  3. GAD65 catalytic-loop mobility favors a side reaction producing succinic semialdehyde and releasing the converted cofactor as PMP.

    Human glutamate decarboxylase 65 / GAD2 → Pyridoxamine 5-prime-phosphate source_derived_draftungraded
    Experimental context and source evidence
    experimental_model
    Recombinant human GAD isoforms; crystallography and enzyme kinetics; Human GAD65/GAD67 recombinant chimeras
    exposure
    Glutamate incubation and enzyme kinetics.
    limitations
    Loop causality is supported by structure and kinetics; cellular net GABA was not measured.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    GAD65 can switch into an inactive cofactor-free form.
    primary_references
    [fenalti-2007-gad] GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop (2007). https://doi.org/10.1038/nsmb1228 DOI: 10.1038/nsmb1228 [langendorf-2013-gad] Structural characterization of the mechanism through which human glutamic acid decarboxylase auto-activates (2013). https://pmc.ncbi.nlm.nih.gov/articles/PMC3546353/ DOI: 10.1042/BSR20120111
    revision_history
    [{"kind": "draft-correction", "description": "Corrected released cofactor identity from PLP to PMP after checking the source; not a scientific conflict."}]
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 973–985

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human GAD isoforms; crystallography and enzyme kinetics; Human GAD65/GAD67 recombinant chimeras · source_derived_draft · unverified_draft

    ### b6-neuro-gad65-autoinactivation GAD65 catalytic-loop mobility favors a side reaction producing succinic semialdehyde and releasing the converted cofactor as PMP. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: GAD65 can switch into an inactive cofactor-free form. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Recombinant human GAD isoforms; crystallography and enzyme kinetics; Human GAD65/GAD67 recombinant chimeras limitations: Loop causality is supported by structure and kinetics; cellular net GABA was not measured. exposure: Glutamate incubation and enzyme kinetics. revision_history: [{"kind": "draft-correction", "description": "Corrected released cofactor identity from PLP to PMP after checking the source; not a scientific conflict."}] [fenalti-2007-gad] GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop (2007). https://doi.org/10.1038/nsmb1228 DOI: 10.1038/nsmb1228 [langendorf-2013-gad] Structural characterization of the mechanism through which human glutamic acid decarboxylase auto-activates (2013). https://pmc.ncbi.nlm.nih.gov/articles/PMC3546353/ DOI: 10.1042/BSR20120111
    Complete structured claim and evidence

  4. Human PNPO also converted PMP to PLP, with a turnover number of 0.20 per second at 37 C.

    Pyridoxine 5-prime-phosphate oxidase / PNPO → Pyridoxamine 5-prime-phosphate source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    A second B6 precursor depends on the FMN enzyme.
    evidence_location
    Results: kinetic properties; Table 1; FMN-binding structure
    experimental_model
    Recombinant human PNPO expressed in E. coli; crystallography and purified-enzyme kinetics at 37 C.
    exposure
    Purified-enzyme assay
    limitations
    Biochemical evidence does not establish a dietary threshold or supplementation benefit.
    nutrient_topic
    Riboflavin research collection; topical membership is not evidence of a direct dietary effect. · Riboflavin (vitamin B2)
    organism
    Homo sapiens
    plain_language
    Phosphorylated pyridoxamine enters the same activation enzyme.
    primary_references
    [musayev2003] Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. (2003). https://pubmed.ncbi.nlm.nih.gov/12824491/ DOI: 10.1110/ps.0356203
    tissue_or_cell_type
    Purified recombinant enzyme; no intact tissue

    Riboflavin: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1164–1176

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human PNPO expressed in E. coli; crystallography and purified-enzyme kinetics at 37 C. · source_derived_draft · unverified_draft

    ### b2-pnpo-pmp-oxidation Human PNPO also converted PMP to PLP, with a turnover number of 0.20 per second at 37 C. Condition category: normal nutrient_topic: Riboflavin research collection; topical membership is not evidence of a direct dietary effect. plain_language: Phosphorylated pyridoxamine enters the same activation enzyme. organism: Homo sapiens tissue_or_cell_type: Purified recombinant enzyme; no intact tissue experimental_model: Recombinant human PNPO expressed in E. coli; crystallography and purified-enzyme kinetics at 37 C. limitations: Biochemical evidence does not establish a dietary threshold or supplementation benefit. exposure: Purified-enzyme assay cross_nutrient: A second B6 precursor depends on the FMN enzyme. evidence_location: Results: kinetic properties; Table 1; FMN-binding structure [musayev2003] Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. (2003). https://pubmed.ncbi.nlm.nih.gov/12824491/ DOI: 10.1110/ps.0356203
    Complete structured claim and evidence

Where it participates (unsigned role)

  1. The human AGXT G82E variant retained two PLP molecules per dimer at saturation but had reduced PLP/PMP affinity and about 0.1% of normal overall catalytic activity.

    Human AGXT G82E catalytic impairment → Human peroxisomal alanine:glyoxylate aminotransferase / AGXT source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    evidence_access
    Primary abstract
    experimental_model
    Purified human disease-associated variant; kinetic and spectroscopic assays.
    limitations
    Not a dietary B6 or alanine deficiency experiment, and not evidence that either supplement rescues this variant.
    nutrient_topic
    L-Alanine collection; species, compartment, exposure, co-substrates and manipulation remain explicit. · L-Alanine
    plain_language
    Having the nutrient available does not guarantee that damaged enzyme machinery can use it.
    primary_references
    Human wild-type alanine:glyoxylate aminotransferase and its naturally occurring G82E variant: functional properties and physiological implications. · 2007 · https://pubmed.ncbi.nlm.nih.gov/17696873/ · DOI 10.1042/BJ20070637
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    L-Alanine: carbon, nitrogen, protein synthesis and cross-nutrient mechanisms (2026-09-19) · lines 48–54

    AI-assisted research curation; primary references, access levels and experimental limitations individually identified. Not publisher full text. · supports · Purified human disease-associated variant; kinetic and spectroscopic assays. · source_derived_draft · unverified_draft

    ## alanine-agt-mutant Having the nutrient available does not guarantee that damaged enzyme machinery can use it. The human AGXT G82E variant retained two PLP molecules per dimer at saturation but had reduced PLP/PMP affinity and about 0.1% of normal overall catalytic activity. Model: Purified human disease-associated variant; kinetic and spectroscopic assays. Limitations: Not a dietary B6 or alanine deficiency experiment, and not evidence that either supplement rescues this variant. Evidence access: Primary abstract Human wild-type alanine:glyoxylate aminotransferase and its naturally occurring G82E variant: functional properties and physiological implications. · 2007 · https://pubmed.ncbi.nlm.nih.gov/17696873/ · DOI 10.1042/BJ20070637
    Complete structured claim and evidence

  2. Human BCAT1 transfers the leucine amino group to 2-oxoglutarate, producing alpha-ketoisocaproate and glutamate.

    Human cytosolic branched-chain aminotransferase / BCAT1 → L-Leucine source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    Essential amino-acid nitrogen transfer; net direction depends on substrate/product conditions.
    experimental_model
    Recombinant human BCAT1 and BCAT2; pre-steady-state kinetics and structures
    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
    B6-dependent transamination starts leucine processing and transfers nitrogen to glutamate.
    primary_references
    [b6-bcat1-2005] Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin (2005). https://pubmed.ncbi.nlm.nih.gov/16141215/ DOI: 10.1074/jbc.M506486200
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 717–727

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human BCAT1 and BCAT2; pre-steady-state kinetics and structures · source_derived_draft · unverified_draft

    ### b6-met-bcat1-leucine Human BCAT1 transfers the leucine amino group to 2-oxoglutarate, producing alpha-ketoisocaproate and glutamate. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: B6-dependent transamination starts leucine processing and transfers nitrogen to glutamate. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Recombinant human BCAT1 and BCAT2; pre-steady-state kinetics and structures limitations: Purified-enzyme evidence does not define dietary requirements or cellular PLP thresholds. cross_nutrient: Essential amino-acid nitrogen transfer; net direction depends on substrate/product conditions. [b6-bcat1-2005] Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin (2005). https://pubmed.ncbi.nlm.nih.gov/16141215/ DOI: 10.1074/jbc.M506486200
    Complete structured claim and evidence

  3. Human BCAT2 transfers the leucine amino group to 2-oxoglutarate, producing alpha-ketoisocaproate and glutamate.

    Human mitochondrial branched-chain aminotransferase / BCAT2 → L-Leucine source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    Essential amino-acid nitrogen transfer; net direction depends on substrate/product conditions.
    experimental_model
    Recombinant human BCAT1 and BCAT2; pre-steady-state kinetics and structures
    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
    B6-dependent transamination starts leucine processing and transfers nitrogen to glutamate.
    primary_references
    [b6-bcat1-2005] Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin (2005). https://pubmed.ncbi.nlm.nih.gov/16141215/ DOI: 10.1074/jbc.M506486200
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 729–739

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human BCAT1 and BCAT2; pre-steady-state kinetics and structures · source_derived_draft · unverified_draft

    ### b6-met-bcat2-leucine Human BCAT2 transfers the leucine amino group to 2-oxoglutarate, producing alpha-ketoisocaproate and glutamate. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: B6-dependent transamination starts leucine processing and transfers nitrogen to glutamate. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Recombinant human BCAT1 and BCAT2; pre-steady-state kinetics and structures limitations: Purified-enzyme evidence does not define dietary requirements or cellular PLP thresholds. cross_nutrient: Essential amino-acid nitrogen transfer; net direction depends on substrate/product conditions. [b6-bcat1-2005] Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin (2005). https://pubmed.ncbi.nlm.nih.gov/16141215/ DOI: 10.1074/jbc.M506486200
    Complete structured claim and evidence

  4. Pyridoxal, pyridoxamine, PLP and PMP did not reduce viability in the tested 24-hour cell assay.

    PLP → SH-SY5Y cell viability by MTT source_derived_draftungraded
    Experimental context and source evidence
    experimental_model
    Differentiated human SH-SY5Y and CaCo-2 cells; isolated enzyme assays
    exposure
    Comparators 0-500 micromolar for 24 hours.
    exposure-class
    Experimental excess pyridoxine; not dietary B6 deficiency · Pyridoxine
    limitations
    A negative short-term cell assay proves neither universal safety nor equivalent toxicity.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    The tested B6 forms behaved differently in this assay.
    primary_references
    [vrolijk-2017-pn] The vitamin B6 paradox: Supplementation with high concentrations of pyridoxine leads to decreased vitamin B6 function (2017). https://doi.org/10.1016/j.tiv.2017.07.009 DOI: 10.1016/j.tiv.2017.07.009
    tissue_or_cell_type
    SH-SY5Y and CaCo-2 cells

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1245–1256

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Differentiated human SH-SY5Y and CaCo-2 cells; isolated enzyme assays · source_derived_draft · unverified_draft

    ### b6-neuro-pn-vitamer-specificity Pyridoxal, pyridoxamine, PLP and PMP did not reduce viability in the tested 24-hour cell assay. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: The tested B6 forms behaved differently in this assay. organism: Homo sapiens tissue_or_cell_type: SH-SY5Y and CaCo-2 cells experimental_model: Differentiated human SH-SY5Y and CaCo-2 cells; isolated enzyme assays limitations: A negative short-term cell assay proves neither universal safety nor equivalent toxicity. exposure: Comparators 0-500 micromolar for 24 hours. exposure-class: Experimental excess pyridoxine; not dietary B6 deficiency [vrolijk-2017-pn] The vitamin B6 paradox: Supplementation with high concentrations of pyridoxine leads to decreased vitamin B6 function (2017). https://doi.org/10.1016/j.tiv.2017.07.009 DOI: 10.1016/j.tiv.2017.07.009
    Complete structured claim and evidence

  5. Purified recombinant human PDXK phosphorylated pyridoxamine to its corresponding 5-prime phosphate.

    Pyridoxal kinase / PDXK → Pyridoxamine source_derived_draftungraded
    Experimental context and source evidence
    evidence_location
    Indexed abstract and publisher abstract; human enzyme findings only
    experimental_model
    Purified recombinant human and E. coli pyridoxal kinases.
    exposure
    Purified-enzyme substrate kinetics.
    limitations
    Model-specific evidence; no dietary threshold or treatment benefit established.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    PDXK adds phosphate to this B6 precursor.
    primary_references
    [disalvo2004] Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases. (2004). https://pubmed.ncbi.nlm.nih.gov/15249053/ DOI: 10.1016/j.pep.2004.04.021
    tissue_or_cell_type
    Purified human enzyme

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 176–187

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified recombinant human and E. coli pyridoxal kinases. · source_derived_draft · unverified_draft

    ### b6-transport-pdxk-pm Purified recombinant human PDXK phosphorylated pyridoxamine to its corresponding 5-prime phosphate. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: PDXK adds phosphate to this B6 precursor. organism: Homo sapiens tissue_or_cell_type: Purified human enzyme experimental_model: Purified recombinant human and E. coli pyridoxal kinases. limitations: Model-specific evidence; no dietary threshold or treatment benefit established. exposure: Purified-enzyme substrate kinetics. evidence_location: Indexed abstract and publisher abstract; human enzyme findings only [disalvo2004] Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases. (2004). https://pubmed.ncbi.nlm.nih.gov/15249053/ DOI: 10.1016/j.pep.2004.04.021
    Complete structured claim and evidence

In the sources

Preserved passages that mention this component, quoted exactly. Open one to read it in context.

    This is a research prototype built from draft material. It is not medical advice, and its statements still await verification against the original studies.

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