Vitamin B6 (pyridoxal 5'-phosphate) salvage and homeostasis (PDXK/PNPO/PDXP)

Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B6 and the obligatory cofactor of ~140 human enzymes — transaminases, decarboxylases, racemases and others across amino-acid, one-carbon, heme and neurotransmitter metabolism. Because humans cannot synthesise the vitamin de novo, PLP is produced and homeostatically balanced by a small salvage pathway that interconverts the dietary B6 vitamers and their phosphorylated forms. Pyridoxal kinase (PDXK) phosphorylates the three unphosphorylated vitamers — pyridoxal, pyridoxine and pyridoxamine — with ATP (and a divalent metal) to pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP). The FMN-dependent pyridoxine 5'-phosphate oxidase (PNPO) then carries out the terminal, rate-limiting step, oxidising PNP and PMP to the active PLP cofactor. Balancing this, the magnesium-dependent pyridoxal phosphatase PDXP (chronophin) dephosphorylates PLP back to pyridoxal, tuning intracellular PLP levels; PDXP also has a well-documented moonlighting role dephosphorylating the actin-regulatory protein cofilin (phospho-Ser3) to promote actin depolymerisation. Inherited PNPO deficiency causes a severe pyridoxal-5'-phosphate-responsive neonatal epileptic encephalopathy, underscoring how tightly neuronal PLP supply depends on this pathway.

MODULE:vitamin_b6_plp_metabolismDRAFTMetabolic Pathwaymodules/vitamin_b6_plp_metabolism.yaml
pyridoxal 5'-phosphate salvageGO:0009443 vitamin B6 metabolic processGO:0042816
GO:0009443
pyridoxal 5'-phosphate salvage
The pathway carries out pyridoxal 5'-phosphate salvage (GO:0009443) from dietary B6 vitamers.
GO:0042816
vitamin B6 metabolic process
It constitutes the core of vitamin B6 metabolic process (GO:0042816) in humans.
file:human/PDXK/PDXK-ai-review.yaml
PDXK gene review (human)
The vitamer-phosphorylation step (UniProtKB:O00764, GO:0008478) matches the completed human PDXK review.
file:human/PNPO/PNPO-ai-review.yaml
PNPO gene review (human)
The PNP/PMP->PLP oxidation step (UniProtKB:Q9NVS9, GO:0004733) matches the completed human PNPO review.
file:human/PDXP/PDXP-ai-review.yaml
PDXP gene review (human)
The PLP dephosphorylation (homeostasis) step (UniProtKB:Q96GD0, GO:0033883) matches the completed human PDXP review.
3Nodes
2Parts
0Variant Sets
0Variants
3Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:vitamin_b6_plp_metabolism deep-research report alongside the module YAML.

Leaf nodes lacking representative members

every leaf node grounds to a representative protein.

Template conformance

every declared conforms_to bundle matches its template motif.

Gene-review completeness (3/3 grounded genes reviewed)

3 complete review(s) · 0 with deep research · 0 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
PDXK O00764
PDXP Q96GD0
PNPO Q9NVS9

Details

Context
cytosolGO:0005829
Vitamin B6 (PLP) salvage and homeostasisMetabolic Pathwayvitamin_b6_plp_metabolism
pyridoxal 5'-phosphate salvageGO:0009443 vitamin B6 metabolic processGO:0042816
Context
cytosolGO:0005829

Vitamin B6 / pyridoxal 5'-phosphate salvage and homeostasis (GO:0009443 / GO:0042816), grounded to the completed human gene reviews: PDXK (O00764, GO:0008478 pyridoxal kinase + Mg/Zn), PNPO (Q9NVS9, GO:0004733 pyridoxamine-phosphate oxidase + FMN GO:0010181, terminal rate-limiting PLP-producing step) and PDXP/chronophin (Q96GD0, GO:0033883 pyridoxal phosphatase + Mg; with a genuine second role as a cofilin/ADF phospho-Ser3 phosphatase, GO:0004721, regulating actin depolymerisation). All three are cytosolic (distinct PANTHER families). PLP is the cofactor of the many PLP-dependent enzymes curated across these modules (transaminases GOT1/2/OAT/AADAT/PSAT1, kynureninase KYNU, serine hydroxymethyltransferases SHMT1/2, etc.). GO term ids/labels verified against the local go.db. Disorders: PNPO deficiency — pyridoxal-5'-phosphate-responsive neonatal epileptic encephalopathy; PDXK variants — polyneuropathy; dysregulated PLP homeostasis affects neurotransmitter (GABA/dopamine/serotonin) synthesis.

Connections

plp_synthesis_salvage -> plp_homeostasis Provides Input For
PDXK/PNPO produce PLP; PDXP dephosphorylates PLP back to pyridoxal, closing the B6-vitamer homeostasis cycle that keeps intracellular PLP within the range required by PLP-dependent enzymes.
Part 1: vitamer phosphorylation and oxidation to PLP
PLP synthesis/salvage (PDXK, PNPO)Reactionplp_synthesis_salvage

Annotons

PDXK: pyridoxal kinase
pdxk_activity
Participant: Family: PDXK / pyridoxal kinase family
Family:
PDXK / pyridoxal kinase familyPANTHER:PTHR10534
Representative Members: PDXK (human)UniProtKB:O00764

Function

pyridoxal kinase activityGO:0008478
Substrates: pyridoxal / pyridoxine / pyridoxamine ATP (with Zn2+/Mg2+)
Products: pyridoxal 5'-phosphate (PLP) / PNP / PMP

Locations

cytosolGO:0005829

Phosphorylates B6 vitamers to their 5'-phosphates.

PNPO: pyridoxine 5'-phosphate oxidase (FMN)
pnpo_activity
Participant: Family: PNPO / pyridoxine-5'-phosphate oxidase family
Family:
PNPO / pyridoxine-5'-phosphate oxidase familyPANTHER:PTHR10851
Representative Members: PNPO (human)UniProtKB:Q9NVS9

Function

pyridoxamine phosphate oxidase activityGO:0004733
Substrates: pyridoxine 5'-phosphate (PNP) / pyridoxamine 5'-phosphate (PMP) O2 (FMN cofactor)
Products: pyridoxal 5'-phosphate (PLP, active cofactor) H2O2

Locations

cytosolGO:0005829

Oxidises PNP/PMP to the active cofactor PLP (rate-limiting).

Part 2: PLP dephosphorylation / homeostasis
PLP homeostasis (PDXP)Reactionplp_homeostasis

Annotons

PDXP (chronophin): pyridoxal phosphatase
pdxp_activity
Participant: Family: PDXP / pyridoxal phosphatase (HAD) family
Family:
PDXP / pyridoxal phosphatase (HAD) familyPANTHER:PTHR19288
Representative Members: PDXP (human)UniProtKB:Q96GD0

Function

pyridoxal phosphatase activityGO:0033883
Substrates: pyridoxal 5'-phosphate (PLP) (Mg2+-dependent)
Products: pyridoxal + phosphate

Locations

cytosolGO:0005829

Dephosphorylates PLP to pyridoxal (homeostasis; also a cofilin phosphatase).