Component

Pyridoxal kinase / PDXK

ATP-dependent B6 vitamer kinase, distinct from PNPO.

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

What it acts on

  1. Purified human PDXK converted ginkgotoxin to its 5-prime-phosphate in an ATP-dependent assay.

    Pyridoxal kinase / PDXK → Ginkgotoxin / 4-prime-O-methylpyridoxine source_derived_draftungraded
    Experimental context and source evidence
    experimental_model
    Purified recombinant human PDXK; HPLC and kinetic competition assays
    exposure
    HPLC product identification at 37 C, pH 6.2.
    limitations
    Purified-enzyme substrate recognition does not establish a whole-body toxicity threshold.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    The toxin can use the B6-activating enzyme.
    primary_references
    [kastner-2007-ginkgotoxin] The human pyridoxal kinase, a plausible target for ginkgotoxin from Ginkgo biloba (2007). https://doi.org/10.1111/j.1742-4658.2007.05654.x DOI: 10.1111/j.1742-4658.2007.05654.x
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1184–1194

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified recombinant human PDXK; HPLC and kinetic competition assays · source_derived_draft · unverified_draft

    ### b6-neuro-ginkgotoxin-phosphorylation Purified human PDXK converted ginkgotoxin to its 5-prime-phosphate in an ATP-dependent assay. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: The toxin can use the B6-activating enzyme. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified recombinant human PDXK; HPLC and kinetic competition assays limitations: Purified-enzyme substrate recognition does not establish a whole-body toxicity threshold. exposure: HPLC product identification at 37 C, pH 6.2. [kastner-2007-ginkgotoxin] The human pyridoxal kinase, a plausible target for ginkgotoxin from Ginkgo biloba (2007). https://doi.org/10.1111/j.1742-4658.2007.05654.x DOI: 10.1111/j.1742-4658.2007.05654.x
    Complete structured claim and evidence

  2. 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

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

    Pyridoxal kinase / PDXK → Pyridoxine 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 163–174

    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-pn Purified recombinant human PDXK phosphorylated pyridoxine 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

  4. Human PDXK assays directly measured ATP-dependent conversion of pyridoxal to PLP, a reaction distinct from PNPO oxidation.

    Pyridoxal kinase / PDXK → Pyridoxal source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    Separates the B6 phosphorylation step from the B2-dependent oxidation step.
    evidence_location
    Abstract
    experimental_model
    Recombinant human PDXK expressed in E. coli; PL-to-PLP kinetics and unliganded/MgATP-bound structures.
    exposure
    Purified-enzyme assay
    limitations
    This biochemical route does not establish that dietary pyridoxal bypasses all consequences of PNPO disease.
    nutrient_topic
    Riboflavin research collection; topical membership is not evidence of a direct dietary effect. · Riboflavin (vitamin B2)
    organism
    Homo sapiens
    plain_language
    Not every route to active B6 passes through PNPO.
    primary_references
    [safo2007] Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. (2007). https://pubmed.ncbi.nlm.nih.gov/17766369/ DOI: 10.1110/ps.073022107
    tissue_or_cell_type
    Purified recombinant enzyme; no intact tissue

    Riboflavin: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1192–1204

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Recombinant human PDXK expressed in E. coli; PL-to-PLP kinetics and unliganded/MgATP-bound structures. · source_derived_draft · unverified_draft

    ### b2-pdxk-pyridoxal-route Human PDXK assays directly measured ATP-dependent conversion of pyridoxal to PLP, a reaction distinct from PNPO oxidation. Condition category: normal nutrient_topic: Riboflavin research collection; topical membership is not evidence of a direct dietary effect. plain_language: Not every route to active B6 passes through PNPO. organism: Homo sapiens tissue_or_cell_type: Purified recombinant enzyme; no intact tissue experimental_model: Recombinant human PDXK expressed in E. coli; PL-to-PLP kinetics and unliganded/MgATP-bound structures. limitations: This biochemical route does not establish that dietary pyridoxal bypasses all consequences of PNPO disease. exposure: Purified-enzyme assay cross_nutrient: Separates the B6 phosphorylation step from the B2-dependent oxidation step. evidence_location: Abstract [safo2007] Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. (2007). https://pubmed.ncbi.nlm.nih.gov/17766369/ DOI: 10.1110/ps.073022107
    Complete structured claim and evidence

What acts on it

  1. Human PDXK crystallography placed ginkgotoxin at the pyridoxal-binding site alongside MgATP.

    Ginkgotoxin / 4-prime-O-methylpyridoxine → Pyridoxal kinase / PDXK source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    experimental_model
    Purified human PDXK; crystallography and inhibition kinetics
    exposure
    2.15 angstrom ternary crystal structure.
    limitations
    Binding in a purified protein does not establish brain concentrations.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    The structure directly locates the competing toxin.
    primary_references
    [gandhi-2012-pdxk-inhibitors] Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition (2012). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040954 DOI: 10.1371/journal.pone.0040954
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1208–1218

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human PDXK; crystallography and inhibition kinetics · source_derived_draft · unverified_draft

    ### b6-neuro-ginkgotoxin-binding Human PDXK crystallography placed ginkgotoxin at the pyridoxal-binding site alongside MgATP. Condition category: machinery_impairment nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: The structure directly locates the competing toxin. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified human PDXK; crystallography and inhibition kinetics limitations: Binding in a purified protein does not establish brain concentrations. exposure: 2.15 angstrom ternary crystal structure. [gandhi-2012-pdxk-inhibitors] Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition (2012). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040954 DOI: 10.1371/journal.pone.0040954
    Complete structured claim and evidence

  2. Ginkgotoxin competed with pyridoxal and delayed PLP formation by human PDXK; increasing pyridoxal alleviated inhibition.

    Ginkgotoxin / 4-prime-O-methylpyridoxine → Pyridoxal kinase / PDXK source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    experimental_model
    Purified recombinant human PDXK; HPLC and kinetic competition assays
    exposure
    25 micromolar pyridoxal with 12.5-25 micromolar ginkgotoxin in illustrative co-incubations.
    limitations
    Reported Ki was assay-specific; not a clinical exposure limit.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    The toxin competes for the enzyme that activates B6.
    primary_references
    [kastner-2007-ginkgotoxin] The human pyridoxal kinase, a plausible target for ginkgotoxin from Ginkgo biloba (2007). https://doi.org/10.1111/j.1742-4658.2007.05654.x DOI: 10.1111/j.1742-4658.2007.05654.x
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1196–1206

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified recombinant human PDXK; HPLC and kinetic competition assays · source_derived_draft · unverified_draft

    ### b6-neuro-ginkgotoxin-plp-competition Ginkgotoxin competed with pyridoxal and delayed PLP formation by human PDXK; increasing pyridoxal alleviated inhibition. Condition category: machinery_impairment nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: The toxin competes for the enzyme that activates B6. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified recombinant human PDXK; HPLC and kinetic competition assays limitations: Reported Ki was assay-specific; not a clinical exposure limit. exposure: 25 micromolar pyridoxal with 12.5-25 micromolar ginkgotoxin in illustrative co-incubations. [kastner-2007-ginkgotoxin] The human pyridoxal kinase, a plausible target for ginkgotoxin from Ginkgo biloba (2007). https://doi.org/10.1111/j.1742-4658.2007.05654.x DOI: 10.1111/j.1742-4658.2007.05654.x
    Complete structured claim and evidence

  3. Theophylline inhibited purified human PDXK, with Ki 50 micromolar, and occupied its vitamin-substrate site.

    Theophylline → Pyridoxal kinase / PDXK source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    experimental_model
    Purified human PDXK; crystallography and inhibition kinetics
    exposure
    Purified-enzyme inhibition series; 2.1 angstrom crystal structure.
    limitations
    Other preparations yielded different Ki values; this is assay context, not a nutritional threshold.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    This drug can interfere with B6 activation in an enzyme assay.
    primary_references
    [gandhi-2012-pdxk-inhibitors] Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition (2012). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040954 DOI: 10.1371/journal.pone.0040954
    tissue_or_cell_type
    Purified recombinant protein; no intact tissue
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 1220–1230

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Purified human PDXK; crystallography and inhibition kinetics · source_derived_draft · unverified_draft

    ### b6-neuro-theophylline-pdxk Theophylline inhibited purified human PDXK, with Ki 50 micromolar, and occupied its vitamin-substrate site. Condition category: machinery_impairment nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: This drug can interfere with B6 activation in an enzyme assay. organism: Homo sapiens tissue_or_cell_type: Purified recombinant protein; no intact tissue experimental_model: Purified human PDXK; crystallography and inhibition kinetics limitations: Other preparations yielded different Ki values; this is assay context, not a nutritional threshold. exposure: Purified-enzyme inhibition series; 2.1 angstrom crystal structure. [gandhi-2012-pdxk-inhibitors] Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition (2012). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040954 DOI: 10.1371/journal.pone.0040954
    Complete structured claim and evidence

  4. Human PDXK showed lower substrate Km with potassium than sodium, whereas sodium supported over twice the maximal activity.

    Potassium ion → Pyridoxal kinase / PDXK source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    Potassium/sodium-B6 enzyme kinetics.
    evidence_location
    Full text: Metal binding and enzyme activity; Figure 1
    experimental_model
    Purified recombinant human PDXK kinetics and crystallography.
    exposure
    Kinetic assays at pH 7.3.
    limitations
    Lower Km is not a direct binding constant; results do not define dietary sodium/potassium effects.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Potassium and sodium affect different kinetic properties.
    primary_references
    [safo2007] Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. (2007). https://pubmed.ncbi.nlm.nih.gov/17766369/ DOI: 10.1110/ps.073022107
    tissue_or_cell_type
    Purified human enzyme

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 203–215

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

    ### b6-transport-pdxk-k-na Human PDXK showed lower substrate Km with potassium than sodium, whereas sodium supported over twice the maximal activity. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Potassium and sodium affect different kinetic properties. organism: Homo sapiens tissue_or_cell_type: Purified human enzyme experimental_model: Purified recombinant human PDXK kinetics and crystallography. limitations: Lower Km is not a direct binding constant; results do not define dietary sodium/potassium effects. exposure: Kinetic assays at pH 7.3. evidence_location: Full text: Metal binding and enzyme activity; Figure 1 cross_nutrient: Potassium/sodium-B6 enzyme kinetics. [safo2007] Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. (2007). https://pubmed.ncbi.nlm.nih.gov/17766369/ DOI: 10.1110/ps.073022107
    Complete structured claim and evidence

  5. Kinase kinetic experiments identified MgATP as the preferred phosphate-donor complex under the reported physiological assay conditions.

    Magnesium-ATP complex → Pyridoxal kinase / PDXK source_derived_draftungraded
    Experimental context and source evidence
    cross_nutrient
    Magnesium-B6 activation chemistry.
    evidence_location
    Indexed abstract and publisher abstract; human enzyme findings only
    experimental_model
    Purified recombinant human and E. coli pyridoxal kinases.
    exposure
    MgATP versus ZnATP kinetic comparisons.
    limitations
    Metal preference depends on assay conditions and does not prove magnesium supplementation improves B6 status.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Magnesium helps supply ATP to B6 activation.
    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 189–201

    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-mgatp Kinase kinetic experiments identified MgATP as the preferred phosphate-donor complex under the reported physiological assay conditions. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Magnesium helps supply ATP to B6 activation. organism: Homo sapiens tissue_or_cell_type: Purified human enzyme experimental_model: Purified recombinant human and E. coli pyridoxal kinases. limitations: Metal preference depends on assay conditions and does not prove magnesium supplementation improves B6 status. exposure: MgATP versus ZnATP kinetic comparisons. evidence_location: Indexed abstract and publisher abstract; human enzyme findings only cross_nutrient: Magnesium-B6 activation chemistry. [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

  6. Homozygous A228T cases had PDXK activities of 0.8 and 1.1 pmol per dried-blood-spot punch per hour; controls ranged 2.6-14.7.

    Human PDXK Ala228Thr homozygous genotype → Pyridoxal kinase / PDXK source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    evidence_location
    Figure 3F; Results
    experimental_model
    Human families, dried blood spots, recombinant PDXK variants.
    exposure
    Patient blood-spot assay.
    limitations
    Assay-specific values.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Inherited activation defects reduced enzyme output.
    primary_references
    [chelban2019] PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation. (2019). https://pubmed.ncbi.nlm.nih.gov/31187503/ DOI: 10.1002/ana.25524
    tissue_or_cell_type
    Erythrocytes
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 230–241

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human families, dried blood spots, recombinant PDXK variants. · source_derived_draft · unverified_draft

    ### b6-transport-pdxk-patient-a228t Homozygous A228T cases had PDXK activities of 0.8 and 1.1 pmol per dried-blood-spot punch per hour; controls ranged 2.6-14.7. Condition category: machinery_impairment nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Inherited activation defects reduced enzyme output. organism: Homo sapiens tissue_or_cell_type: Erythrocytes experimental_model: Human families, dried blood spots, recombinant PDXK variants. limitations: Assay-specific values. exposure: Patient blood-spot assay. evidence_location: Figure 3F; Results [chelban2019] PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation. (2019). https://pubmed.ncbi.nlm.nih.gov/31187503/ DOI: 10.1002/ana.25524
    Complete structured claim and evidence

  7. Homozygous R220Q cases had PDXK activities of 0.5 and 1.19 pmol per dried-blood-spot punch per hour; controls ranged 2.6-14.7.

    Human PDXK Arg220Gln homozygous genotype → Pyridoxal kinase / PDXK source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    evidence_location
    Figure 3F; Results
    experimental_model
    Human families, dried blood spots, recombinant PDXK variants.
    exposure
    Patient blood-spot assay.
    limitations
    Assay-specific values.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Inherited activation defects reduced enzyme output.
    primary_references
    [chelban2019] PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation. (2019). https://pubmed.ncbi.nlm.nih.gov/31187503/ DOI: 10.1002/ana.25524
    tissue_or_cell_type
    Erythrocytes
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 243–254

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human families, dried blood spots, recombinant PDXK variants. · source_derived_draft · unverified_draft

    ### b6-transport-pdxk-patient-r220q Homozygous R220Q cases had PDXK activities of 0.5 and 1.19 pmol per dried-blood-spot punch per hour; controls ranged 2.6-14.7. Condition category: machinery_impairment nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Inherited activation defects reduced enzyme output. organism: Homo sapiens tissue_or_cell_type: Erythrocytes experimental_model: Human families, dried blood spots, recombinant PDXK variants. limitations: Assay-specific values. exposure: Patient blood-spot assay. evidence_location: Figure 3F; Results [chelban2019] PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation. (2019). https://pubmed.ncbi.nlm.nih.gov/31187503/ DOI: 10.1002/ana.25524
    Complete structured claim and evidence

Where it participates (unsigned role)

  1. Polarized Caco-2 cells supplied apically with PM generated PL and released more PL basolaterally than apically.

    Pyridoxamine → Pyridoxal source_derived_draftungraded
    Experimental context and source evidence
    evidence_location
    Results: Incubation with pyridoxamine; Figure 4
    experimental_model
    Polarized human Caco-2 monolayers; human intestinal lysates.
    exposure
    100 or 1000 nM PM; 6-48 h.
    limitations
    Vitamer measurements establish net conversion; individual enzyme fluxes were not separately perturbed.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Enterocytes can process a precursor before releasing pyridoxal.
    primary_references
    [albersen2013] The intestine plays a substantial role in human vitamin B6 metabolism: a Caco-2 cell model. (2013). https://pubmed.ncbi.nlm.nih.gov/23342087/ DOI: 10.1371/journal.pone.0054113
    tissue_or_cell_type
    Polarized Caco-2 monolayers

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 137–148

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Polarized human Caco-2 monolayers; human intestinal lysates. · source_derived_draft · unverified_draft

    ### b6-transport-enterocyte-pm-to-pl Polarized Caco-2 cells supplied apically with PM generated PL and released more PL basolaterally than apically. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Enterocytes can process a precursor before releasing pyridoxal. organism: Homo sapiens tissue_or_cell_type: Polarized Caco-2 monolayers experimental_model: Polarized human Caco-2 monolayers; human intestinal lysates. limitations: Vitamer measurements establish net conversion; individual enzyme fluxes were not separately perturbed. exposure: 100 or 1000 nM PM; 6-48 h. evidence_location: Results: Incubation with pyridoxamine; Figure 4 [albersen2013] The intestine plays a substantial role in human vitamin B6 metabolism: a Caco-2 cell model. (2013). https://pubmed.ncbi.nlm.nih.gov/23342087/ DOI: 10.1371/journal.pone.0054113
    Complete structured claim and evidence

  2. Polarized Caco-2 cells supplied apically with PN generated PL and released more PL basolaterally than apically.

    Pyridoxine → Pyridoxal source_derived_draftungraded
    Experimental context and source evidence
    evidence_location
    Results: Incubation with pyridoxine; Figure 4
    experimental_model
    Polarized human Caco-2 monolayers; human intestinal lysates.
    exposure
    100 or 1000 nM PN; 6-48 h.
    limitations
    Vitamer measurements establish net conversion; individual enzyme fluxes were not separately perturbed.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Enterocytes can process a precursor before releasing pyridoxal.
    primary_references
    [albersen2013] The intestine plays a substantial role in human vitamin B6 metabolism: a Caco-2 cell model. (2013). https://pubmed.ncbi.nlm.nih.gov/23342087/ DOI: 10.1371/journal.pone.0054113
    tissue_or_cell_type
    Polarized Caco-2 monolayers

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 124–135

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Polarized human Caco-2 monolayers; human intestinal lysates. · source_derived_draft · unverified_draft

    ### b6-transport-enterocyte-pn-to-pl Polarized Caco-2 cells supplied apically with PN generated PL and released more PL basolaterally than apically. Condition category: normal nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Enterocytes can process a precursor before releasing pyridoxal. organism: Homo sapiens tissue_or_cell_type: Polarized Caco-2 monolayers experimental_model: Polarized human Caco-2 monolayers; human intestinal lysates. limitations: Vitamer measurements establish net conversion; individual enzyme fluxes were not separately perturbed. exposure: 100 or 1000 nM PN; 6-48 h. evidence_location: Results: Incubation with pyridoxine; Figure 4 [albersen2013] The intestine plays a substantial role in human vitamin B6 metabolism: a Caco-2 cell model. (2013). https://pubmed.ncbi.nlm.nih.gov/23342087/ DOI: 10.1371/journal.pone.0054113
    Complete structured claim and evidence

  3. ATPgammaS binding was detected for wild-type PDXK but not A228T under the ITC conditions; A228T also required higher MgATP for half-maximal activity.

    Human PDXK Ala228Thr → ATP gamma S source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    evidence_location
    Figure 3B,E
    experimental_model
    Human families, dried blood spots, recombinant PDXK variants.
    exposure
    ATPgammaS ITC; variable MgATP kinetics.
    limitations
    ATPgammaS is an analog; absence of detectable binding is assay-specific.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    The variant disrupts nucleotide handling.
    primary_references
    [chelban2019] PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation. (2019). https://pubmed.ncbi.nlm.nih.gov/31187503/ DOI: 10.1002/ana.25524
    tissue_or_cell_type
    Purified human enzyme
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 217–228

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human families, dried blood spots, recombinant PDXK variants. · source_derived_draft · unverified_draft

    ### b6-transport-pdxk-a228t-atp ATPgammaS binding was detected for wild-type PDXK but not A228T under the ITC conditions; A228T also required higher MgATP for half-maximal activity. Condition category: machinery_impairment nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: The variant disrupts nucleotide handling. organism: Homo sapiens tissue_or_cell_type: Purified human enzyme experimental_model: Human families, dried blood spots, recombinant PDXK variants. limitations: ATPgammaS is an analog; absence of detectable binding is assay-specific. exposure: ATPgammaS ITC; variable MgATP kinetics. evidence_location: Figure 3B,E [chelban2019] PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation. (2019). https://pubmed.ncbi.nlm.nih.gov/31187503/ DOI: 10.1002/ana.25524
    Complete structured claim and evidence

  4. After a 100 nM D3-PN pulse, labeled PLP appeared in whole cells but scarcely in SLC25A38-null mitochondria.

    Human SLC25A38 knockout genotype → PLP source_derived_draftungraded
    Experimental context and source evidence
    availability_state
    machinery_impairment Imported condition classification; unverified.
    evidence_location
    Figure 4A-B
    experimental_model
    Human K562 knockout cells, Mito-IP, LC-MS and isotope tracing.
    exposure
    100 nM D3-PN, one-hour tracing after 10 nM PN conditioning.
    limitations
    Import, retention and indirect regulation remain alternatives.
    nutrient_topic
    Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. · Vitamin B6
    organism
    Homo sapiens
    plain_language
    Synthesis persisted while mitochondrial accumulation failed.
    primary_references
    [pena2025] SLC25A38 is required for mitochondrial pyridoxal 5'-phosphate (PLP) accumulation. (2025). https://pubmed.ncbi.nlm.nih.gov/39856062/ DOI: 10.1038/s41467-025-56130-3
    tissue_or_cell_type
    K562 cells
    trigger_kind
    machinery_impairment Imported condition classification; unverified.

    Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17) · lines 465–476

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Human K562 knockout cells, Mito-IP, LC-MS and isotope tracing. · source_derived_draft · unverified_draft

    ### b6-transport-slc25a38-tracer After a 100 nM D3-PN pulse, labeled PLP appeared in whole cells but scarcely in SLC25A38-null mitochondria. Condition category: machinery_impairment nutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect. plain_language: Synthesis persisted while mitochondrial accumulation failed. organism: Homo sapiens tissue_or_cell_type: K562 cells experimental_model: Human K562 knockout cells, Mito-IP, LC-MS and isotope tracing. limitations: Import, retention and indirect regulation remain alternatives. exposure: 100 nM D3-PN, one-hour tracing after 10 nM PN conditioning. evidence_location: Figure 4A-B [pena2025] SLC25A38 is required for mitochondrial pyridoxal 5'-phosphate (PLP) accumulation. (2025). https://pubmed.ncbi.nlm.nih.gov/39856062/ DOI: 10.1038/s41467-025-56130-3
    Complete structured claim and evidence

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