DXP-dependent de novo pyridoxal 5'-phosphate biosynthesis

De novo synthesis of pyridoxal 5'-phosphate (PLP, vitamin B6) through the DXP-dependent bacterial pathway. One branch converts D-erythrose 4-phosphate to 3-amino-2-oxopropyl phosphate through Epd, PdxB, SerC, and PdxA. PdxJ then condenses this product with the shared metabolite 1-deoxy-D-xylulose 5-phosphate (DXP) to form pyridoxine 5'-phosphate, and PdxH performs the terminal oxidation to PLP. DXP production is shared with thiamine and isoprenoid metabolism and is outside this module boundary. The alternative DXP-independent PdxS/PdxT pathway and vitamin-B6 salvage are separate modules.

MODULE:pyridoxal_5_phosphate_biosynthesisDRAFTMetabolic Pathwaymodules/pyridoxal_5_phosphate_biosynthesis.yaml
'de novo' pyridoxal 5'-phosphate biosynthetic processGO:0036001
GO:0036001
'de novo' pyridoxal 5'-phosphate biosynthetic process
The module is grounded in the GO biological process for de novo PLP biosynthesis.
UniPathway:UPA00244
Pyridoxine 5'-phosphate biosynthesis
UniPathway orders the Epd/PdxB/SerC/PdxA/PdxJ branch that forms pyridoxine 5'-phosphate from D-erythrose 4-phosphate and DXP.
KEGG:ppu00750
Pseudomonas putida KT2440 vitamin B6 metabolism
The PSEPK pathway instance contains the six de novo-pathway proteins used as exemplars, as well as salvage enzymes and unrelated PLP-dependent pathway-map members that are outside this module boundary.
PMID:10885790
Biosynthesis of pyridoxine: origin of the nitrogen atom of pyridoxine in microorganisms.
Species-level isotope-labeling evidence places Pseudomonas putida in the glutamate-nitrogen, DXP-dependent pyridoxine-biosynthesis route.
the nitrogen atom of glutamate was incorporated into pyridoxine in P. putida, E. aerogenes and E. coli
file:projects/P_PUTIDA/deep-research/PSEPK__dxp-dependent-pyridoxal-5-phosphate-biosynthesis__ppu00750-deep-research-openscientist.md
OpenScientist module/pathway/taxon report for PSEPK DXP-dependent PLP biosynthesis
Supports the six-step de novo pathway, its external DXP dependency, exclusion of salvage and PLP-consuming threonine synthases, and complete satisfiability in KT2440. Gene-level biochemical assignments remain homology-inferred.
file:projects/P_PUTIDA/data/psepk_pathway_membership.tsv
PSEPK pathway membership table
The local pathway partition supplies the PSEPK accessions and locus tags used for the module exemplars.
7Nodes
6Parts
0Variant Sets
0Variants
6Annotons
5Connections

Derived QC

Recommended-field compliance

55.6% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)

Module deep research

✗ none found

No MODULE:pyridoxal_5_phosphate_biosynthesis 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.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • epd_step → pdxB_step [NOT_CHECKED]
  • pdxB_step → serC_step [NOT_CHECKED]
  • serC_step → pdxA_step [NOT_CHECKED]
  • pdxA_step → pdxJ_step [NOT_CHECKED]
  • pdxJ_step → pdxH_step [NOT_CHECKED]

Gene-review completeness (6/6 grounded genes reviewed)

6 complete review(s) · 5 with deep research · 0 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
epd Q88D63 ✓ ✓ ✓
pdxA Q88QT5 ✓ ✓ ✓
pdxB Q88L20 ✓ ✓ ✓
pdxH Q88NS5 ✓ ✓ ✓
pdxJ Q88MY2 ✓ ✓ ✗
serC Q88M07 ✓ ✓ ✓

Details

DXP-dependent de novo PLP biosynthesisMetabolic Pathwaypyridoxal_5_phosphate_biosynthesis
'de novo' pyridoxal 5'-phosphate biosynthetic processGO:0036001

The reusable module is defined by reaction chemistry rather than PSEPK gene names. All molecular functions are on leaf annotons, every leaf has a concrete PSEPK UniProt exemplar, and no redundant cytoplasm/cytosol context is asserted. Epd and SerC are shared-metabolism enzymes, PdxH also supports salvage, and DXP supply is an upstream input rather than an extra module part. Species-level isotope labeling in P. putida independently supports use of the glutamate-nitrogen DXP-dependent route, but it is not treated as a direct assay of the six KT2440 proteins.

Connections

epd_step -> pdxB_step Precedes
pdxB_step -> serC_step Precedes
serC_step -> pdxA_step Precedes
pdxA_step -> pdxJ_step Precedes
pdxJ_step -> pdxH_step Precedes
Part 1: erythrose 4-phosphate oxidation
D-erythrose 4-phosphate to 4-phospho-D-erythronateReactionepd_step

Annotons

Erythrose-4-phosphate dehydrogenase
epd_activity
Participant: Family: bacterial Epd family
Family:
bacterial Epd familyNCBIfam:TIGR01532
Representative Members: PSEPK EpdUniProtKB:Q88D63
Required Function:
erythrose-4-phosphate dehydrogenase activityGO:0048001

Function

erythrose-4-phosphate dehydrogenase activityGO:0048001
Substrates: D-erythrose 4-phosphate NAD+ water
Products: 4-phospho-D-erythronate NADH

Produces the four-carbon phosphoerythronate branch intermediate from pentose-phosphate-pathway-derived erythrose 4-phosphate.

Part 2: phosphoerythronate oxidation
4-phospho-D-erythronate to 3-hydroxy-2-oxo-4-phosphooxybutanoateReactionpdxB_step

Annotons

PdxB 4-phosphoerythronate dehydrogenase
pdxB_activity
Participant: Family: PdxB erythronate-4-phosphate dehydrogenase family
Family:
PdxB erythronate-4-phosphate dehydrogenase familyInterPro:IPR020921
Representative Members: PSEPK PdxBUniProtKB:Q88L20
Required Function:
4-phosphoerythronate dehydrogenase activityGO:0033711

Function

4-phosphoerythronate dehydrogenase activityGO:0033711
Substrates: 4-phospho-D-erythronate NAD+
Products: (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate NADH

Generates the keto-acid substrate for the following SerC transamination.

Part 3: phosphohydroxythreonine formation
3-hydroxy-2-oxo-4-phosphooxybutanoate to 4-phosphohydroxy-L-threonineReactionserC_step

Annotons

SerC phosphohydroxythreonine aminotransferase
serC_activity
Participant: Family: SerC phosphoserine aminotransferase family
Family:
SerC phosphoserine aminotransferase familyPANTHER:PTHR43247:SF1
Representative Members: PSEPK SerCUniProtKB:Q88M07
Required Function:
phosphohydroxythreonine aminotransferase activity

Function

phosphohydroxythreonine aminotransferase activity
Substrates: (R)-3-hydroxy-2-oxo-4-phosphooxybutanoate L-glutamate
Products: 4-(phosphooxy)-L-threonine 2-oxoglutarate

Shared SerC chemistry supplies both serine biosynthesis and this PLP-biosynthesis branch; the enzyme is not PLP-pathway-specific.

Part 4: aminoacetone-phosphate formation
4-phosphohydroxy-L-threonine to 3-amino-2-oxopropyl phosphateReactionpdxA_step

Annotons

PdxA 4-hydroxythreonine-4-phosphate dehydrogenase
pdxA_activity
Participant: Family: PdxA family
Family:
PdxA familyPANTHER:PTHR30004:SF5
Representative Members: PSEPK PdxAUniProtKB:Q88QT5
Required Function:
4-hydroxythreonine-4-phosphate dehydrogenase activityGO:0050570

Function

4-hydroxythreonine-4-phosphate dehydrogenase activityGO:0050570
Substrates: 4-(phosphooxy)-L-threonine NAD+
Products: 3-amino-2-oxopropyl phosphate carbon dioxide NADH

Oxidation followed by spontaneous decarboxylation produces the aminoacetone-phosphate branch substrate used by PdxJ.

Part 5: pyridoxine 5'-phosphate ring formation
3-amino-2-oxopropyl phosphate and DXP to pyridoxine 5'-phosphateReactionpdxJ_step

Annotons

PdxJ pyridoxine 5'-phosphate synthase
pdxJ_activity
Participant: Family: PdxJ family
Family:
PdxJ familyPANTHER:PTHR30456:SF0
Representative Members: PSEPK PdxJUniProtKB:Q88MY2
Required Function:
pyridoxine 5'-phosphate synthase activityGO:0033856

Function

pyridoxine 5'-phosphate synthase activityGO:0033856
Substrates: 3-amino-2-oxopropyl phosphate 1-deoxy-D-xylulose 5-phosphate
Products: pyridoxine 5'-phosphate phosphate water

Joins the erythrose-derived branch product with the shared DXP input to construct the vitamin-B6 ring.

Part 6: terminal PLP formation
Pyridoxine 5'-phosphate to pyridoxal 5'-phosphateReactionpdxH_step

Annotons

PdxH pyridoxine/pyridoxamine 5'-phosphate oxidase
pdxH_activity
Participant: Family: PdxH/PNPO family
Family:
PdxH/PNPO familyPANTHER:PTHR10851:SF0
Representative Members: PSEPK PdxHUniProtKB:Q88NS5
Required Function:
pyridoxamine phosphate oxidase activityGO:0004733

Function

pyridoxamine phosphate oxidase activityGO:0004733
Substrates: pyridoxine 5'-phosphate or pyridoxamine 5'-phosphate oxygen
Products: pyridoxal 5'-phosphate hydrogen peroxide

FMN-dependent terminal oxidation produces the active PLP cofactor; the same enzyme also participates in vitamin-B6 salvage.