Pseudomonas pyoverdine non-proteinogenic precursor supply

A reusable Pseudomonas module for reactions that supply unusual amino-acid building blocks to the cytoplasmic pyoverdine NRPS assembly line. PvdA hydroxylates L-ornithine to produce N5-hydroxy-L-ornithine, and PvdH forms L-2,4-diaminobutyrate from L-aspartate 4-semialdehyde by PLP-dependent transamination. Hydroxyornithine acylation, NRPS assembly, ferribactin export, periplasmic maturation, secretion, ferripyoverdine uptake, and iron release are outside this module.

MODULE:pseudomonas_pyoverdine_precursor_supplyDRAFTCONCRETEBiological Processmodules/pseudomonas_pyoverdine_precursor_supply.yaml
pyoverdine biosynthetic processGO:0002049
PMID:8106324
Cloning and nucleotide sequence of the pvdA gene encoding the pyoverdin biosynthetic enzyme L-ornithine N5-oxygenase in Pseudomonas aeruginosa.
Establishes PvdA-dependent ornithine N5-hydroxylation as an early pyoverdine biosynthetic step.
PMID:15317763
Functional characterization of an aminotransferase required for pyoverdine siderophore biosynthesis in Pseudomonas aeruginosa PAO1.
Establishes PvdH-dependent L-2,4-diaminobutyrate formation and its requirement for pyoverdine biosynthesis.
PMID:19459056
Siderophore-mediated iron acquisition in the entomopathogenic bacterium Pseudomonas entomophila L48 and its close relative Pseudomonas putida KT2440.
Establishes that Pseudomonas putida KT2440 produces a characterized pyoverdine.
file:modules/pseudomonas_pyoverdine_precursor_supply-deep-research-openscientist.md
OpenScientist research for Pseudomonas pyoverdine precursor supply
Evaluates the PvdA/PvdH two-reaction boundary, reaction chemistry, conservation, and distinction from adjacent tailoring and assembly.
file:projects/P_PUTIDA/deep-research/PSEPK__pseudomonas_pyoverdine_precursor_supply__ppu00975-deep-research-openscientist.md
OpenScientist PSEPK satisfiability review for pyoverdine precursor supply
Finds both module reactions covered in KT2440 by pvdA/PP_3796 and pvdH/PP_4223, while identifying pvdA as a KEGG-bucket omission, PP_2800 as paralog spillover, and PvdY as adjacent tailoring.

The module is limited to precursor-supply chemistry shared across pyoverdine-producing Pseudomonas. KT2440 proteins are exemplars, while the direct biochemical evidence for PvdA and PvdH comes primarily from Pseudomonas aeruginosa homologs. No PANTHER selector is asserted because the unreviewed KT2440 accessions are not present in the local PANTHER member index. PvdY hydroxyornithine acetylation is adjacent tailoring rather than a precursor-forming reaction and remains outside this strict module boundary. PP_2800 is outside the module unless evidence distinguishes it from the dedicated cluster enzyme PvdH.

3Nodes
2Parts
0Variant Sets
0Variants
2Annotons
0Connections

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

✓ present

  • pseudomonas_pyoverdine_precursor_supply-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.

Gene-review completeness (2/2 grounded genes reviewed)

2 complete review(s) · 2 with deep research · 0 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
pvdA Q88GC8 ✓ ✓ ✓
pvdH Q88F75 ✓ ✓ ✓

Details

Context
PseudomonasNCBITaxon:286
Pseudomonas pyoverdine non-proteinogenic precursor supplyBiological Processpseudomonas_pyoverdine_precursor_supply
pyoverdine biosynthetic processGO:0002049
Context
PseudomonasNCBITaxon:286
Part 1: N5-hydroxy-L-ornithine precursor supply
PvdA-dependent ornithine N5-hydroxylationReactionpvda_ornithine_hydroxylation

Annotons

Pyoverdine ornithine N5-monooxygenase PvdA
pvda_ornithine_n5_monooxygenase
Participant: Family: Pseudomonas pyoverdine PvdA ornithine N5-monooxygenase family
Family:
Pseudomonas pyoverdine PvdA ornithine N5-monooxygenase family
Representative Members: PvdA (Pseudomonas putida KT2440)UniProtKB:Q88GC8

Function

ornithine N5-monooxygenase activityGO:0031172
Substrates: L-ornithine
Products: N5-hydroxy-L-ornithine

Processes

pyoverdine biosynthetic processGO:0002049

Locations

cytoplasmGO:0005737

Produces hydroxylated ornithine for subsequent acylation and incorporation into the pyoverdine peptide precursor.

Part 2: L-2,4-diaminobutyrate precursor supply
PvdH-dependent L-2,4-diaminobutyrate formationReactionpvdh_diaminobutyrate_formation

Annotons

Pyoverdine diaminobutyrate transaminase PvdH
pvdh_diaminobutyrate_transaminase
Participant: Family: Pseudomonas pyoverdine PvdH diaminobutyrate transaminase family
Family:
Pseudomonas pyoverdine PvdH diaminobutyrate transaminase family
Representative Members: PvdH (Pseudomonas putida KT2440)UniProtKB:Q88F75

Function

L-2,4-diaminobutyrate:2-oxoglutarate transaminase activityGO:0045303
Substrates: L-aspartate 4-semialdehyde L-glutamate
Products: L-2,4-diaminobutyrate 2-oxoglutarate

Processes

pyoverdine biosynthetic processGO:0002049

Locations

cytoplasmGO:0005737

Produces L-2,4-diaminobutyrate for incorporation into the strain-specific pyoverdine peptide precursor.