kdsA1

UniProt ID: Q88MG0
Organism: Pseudomonas putida KT2440
Review Status: COMPLETE
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Gene Description

KdsA1 is a cytoplasmic KDO-8-phosphate synthase that condenses D-arabinose-5-phosphate with phosphoenolpyruvate to form KDO-8-phosphate. It is one of two KT2440 KdsA paralogs supplying KDO for lipopolysaccharide.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005737 cytoplasm
IEA
GO_REF:0000120 		MODIFY
Summary: KdsA1 is a soluble cytoplasmic enzyme; cytosol is the more specific location.
Reason: Correct but general. KdsA1 has no membrane-anchoring feature and belongs to the KdsA subfamily whose PAINT root node (PTN000471837) carries cytosol, seeded by direct fractionation evidence for E. coli KdsA; cytosol is the part_of descendant that fits this soluble enzyme.
Proposed replacements: cytosol
Supporting Evidence:
file:PSEPK/kdsA1/kdsA1-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|PROSITE-ProRule:PRU01406}
file:interpro/panther/PTHR21057/PTHR21057-paint.tsv
PTHR21057 PTN000471837 GO:0005829 C IBD false UniProtKB:P0A715
GO:0008676 3-deoxy-8-phosphooctulonate synthase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: KdsA1 condenses D-arabinose 5-phosphate with phosphoenolpyruvate to KDO 8-phosphate.
Reason: HAMAP MF_00056, NCBIfam TIGR01362 and the PTHR21057 family, whose every tree leaf is a KdsA-type enzyme and whose root carries this activity by PAINT, agree on the exact reaction.
Supporting Evidence:
file:PSEPK/kdsA1/kdsA1-uniprot.txt
DR HAMAP; MF_00056; KDO8P_synth; 1.
file:PSEPK/kdsA1/kdsA1-uniprot.txt
Reaction=D-arabinose 5-phosphate + phosphoenolpyruvate + H2O
GO:0009103 lipopolysaccharide biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: KDO 8-phosphate is the precursor of the KDO residues of the LPS inner core.
Reason: KdsA1 performs a step of the pathway that makes the KDO moiety of LPS; GO:0019294 has GO:0009103 among its ancestors, so the row agrees with the core process. It is kept as ACCEPT rather than refined because lipopolysaccharide biosynthesis is itself a core process of this gene (listed in core_functions.directly_involved_in), not a too-general stand-in for KDO biosynthesis.
Supporting Evidence:
file:PSEPK/kdsA1/kdsA1-uniprot.txt
DR HAMAP; MF_00056; KDO8P_synth; 1.
PMID:10734095
KDO8P is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the lipopolysaccharide of Gram-negative bacteria
GO:0019294 keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
IEA
GO_REF:0000104 		ACCEPT
Summary: KDO 8-phosphate synthesis is the second step of KDO biosynthesis.
Reason: The UniRule transfer agrees with the HAMAP KdsA family and the E. coli KdsA enzymology.
Supporting Evidence:
file:PSEPK/kdsA1/kdsA1-uniprot.txt
3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate
GO:0046394 carboxylic acid biosynthetic process
IEA
GO_REF:0000117 		MODIFY
Summary: KDO is an ulosonic (carboxylic) acid; the ARBA call is true but generic.
Reason: Correct but general; KDO biosynthetic process (GO:0019294), which the gene also carries, is an is_a descendant of carboxylic acid biosynthetic process.
Supporting Evidence:
file:PSEPK/kdsA1/kdsA1-uniprot.txt
3-deoxy-D-manno-octulosonate from D-ribulose 5-phosphate

Core Functions

KDO-8-phosphate synthase (EC 2.5.1.55; Rhea 14053), condensing D-arabinose-5-phosphate and phosphoenolpyruvate in CMP-KDO biosynthesis.

Molecular Function:
3-deoxy-8-phosphooctulonate synthase activity
Directly Involved In:
keto-3-deoxy-D-manno-octulosonic acid biosynthetic process lipopolysaccharide biosynthetic process
Cellular Locations:
cytosol
Supporting Evidence:
  • file:PSEPK/kdsA1/kdsA1-uniprot.txt
    Reaction=D-arabinose 5-phosphate + phosphoenolpyruvate + H2O

References

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Suggested Questions for Experts

Q: Are kdsA1 and kdsA2 differentially expressed during changes in surface-polysaccharide production?

Suggested Experiments

Experiment: Compare expression and CMP-KDO pools in kdsA1 and kdsA2 single mutants.

Type: transcript profiling and targeted metabolomics

📚 Additional Documentation

Notes

(kdsA1-notes.md)

kdsA1 curation notes

  • The reviewed Q88MG0 record carries the exact EC 2.5.1.55/Rhea 14053
    KDO-8-phosphate synthase reaction [file:PSEPK/kdsA1/kdsA1-uniprot.txt,
    "Reaction=D-arabinose 5-phosphate + phosphoenolpyruvate + H2O"].
  • KT2440 also encodes kdsA2. Both exact activity assignments are accepted, but
    their physiological division of labor remains untested.

2026-11-10 completion pass

  • Generic parent rows that the evidence refines were changed to MODIFY with the
    specific KDO-pathway term (rather than MARK_AS_OVER_ANNOTATED), matching the
    E. coli exemplar reviews; substrate-binding rows stay KEEP_AS_NON_CORE.
  • Every row now carries a vetted quote (UniProt curated rule/family lines,
    PANTHER PAINT rows, or E. coli ortholog papers clearly marked as such).
  • No provider deep research was generated (no provider access in this session).

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