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.
file:modules/pyridoxal_5_phosphate_biosynthesis-deep-research-openscientist.md
OpenScientist review of DXP-dependent de novo PLP biosynthesis
Independent retrieval supports the fixed Epd-PdxB-SerC-PdxA-PdxJ-PdxH sequence and treats DXP supply, vitamin-B6 salvage, and the non-homologous PdxS/PdxT route as separate biological systems.
file:projects/P_PUTIDA/data/psepk_pathway_membership.tsv
PSEPK pathway membership table
The deterministic pathway partition supplies the PSEPK accessions and locus tags used for the six pathway-instance exemplars.
7Nodes
6Parts
0Variant Sets
0Variants
6Annotons
5Connections

Derived QC

Recommended-field compliance

60.0% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)

Module deep research

✓ present

  • pyridoxal_5_phosphate_biosynthesis-deep-research-openscientist.md (openscientist)

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 (6/12 grounded genes reviewed)

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

Gene Review Complete Deep research
epd Q88D63 ✓ ✓ ✓
Escherichia coli K-12 PdxB P05459 ✗ — —
Escherichia coli K-12 PdxJ P0A794 ✗ — —
Escherichia coli K-12 Epd P0A9B6 ✗ — —
Escherichia coli K-12 PdxH P0AFI7 ✗ — —
Escherichia coli K-12 PdxA P19624 ✗ — —
Escherichia coli K-12 SerC P23721 ✗ — —
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 and uses reviewed cross-species UniProt exemplars. All molecular functions are on leaf annotons, and no generic localization 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. The DXP-independent PdxS/PdxT route and vitamin-B6 salvage are outside this module boundary.

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: Escherichia coli K-12 EpdUniProtKB:P0A9B6 Pseudomonas putida KT2440 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: Escherichia coli K-12 PdxBUniProtKB:P05459 Pseudomonas putida KT2440 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: Escherichia coli K-12 SerCUniProtKB:P23721 Pseudomonas putida KT2440 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: Escherichia coli K-12 PdxAUniProtKB:P19624 Pseudomonas putida KT2440 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: Escherichia coli K-12 PdxJUniProtKB:P0A794 Pseudomonas putida KT2440 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: Escherichia coli K-12 PdxHUniProtKB:P0AFI7 Pseudomonas putida KT2440 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.