prpC (PA0795, Q9I5E3) review notes

Literature

Searches 2026-11-05: PubMed MCP search failing (API errors); web search
"Pseudomonas aeruginosa methylcitrate synthase PrpC PA0795" found the Dolan et al. 2022
mBio paper (DOI 10.1128/mbio.02541-22 = PMID:36377867, PMC9765439, full text cached) and
PDB 6S6F/6S87 (PrpC apo and oxaloacetate-bound).

  1. Mitchell et al. 1995 PMID:7626013. Abstract only (PMC1135760 is a scanned PDF; the
    PMC full-text call returned no text). Two native citrate synthases purified from
    P. aeruginosa: CSI, a hexamer of 42-kDa subunits, and CSII, a dimer of 36.5-kDa
    subunits PMID:7626013. No gene is
    identified PMID:7626013. The paper predates the PAO1 genome (2000).
    PseudoCAP annotated the same IDA rows (GO:0036440, GO:0006099) to both gltA (P14165)
    and prpC (Q9I5E3) (.cache/paint/pseudocap.tsv).
  2. Dolan et al. 2022 PMID:36377867, full text cached. Purified PrpC has both citrate
    synthase and 2-methylcitrate synthase activity PMID:36377867, with roughly comparable
    activity toward both acyl-CoAs and higher Vmax with propionyl-CoA. PrpC is a homodimer
    PMID:36377867, GltA a hexamer; monomer mass about 41 kDa.
    ΔprpC cannot grow on propionate PMID:36377867. Basal PrpC
    rescues ΔgltA, and a ΔgltA ΔprpC double mutant could not be made PMID:36377867.

Interpretation: CSII of the 1995 paper (dimer, ~37-41 kDa subunit) matches PrpC, and CSI
(hexamer) matches GltA, so PseudoCAP's attribution is very likely right in substance, but
the 1995 paper itself cannot tie either enzyme to a gene. PrpC's citrate synthase
activity is a genuine secondary activity: comparable kcat with acetyl-CoA, and enough
in vivo to keep a gltA mutant alive. Its main role is 2-methylcitrate synthesis in the
2-methylcitrate cycle (propionate catabolism).

PseudoCAP IBA-seed assessment

PTN node node term n_seeds leaf IBAs seed annotation (term, evidence, PMID) verdict rationale other seeds IBD stands without this seed?
PTN000201223 GO:0036440 citrate synthase activity 19 270 (123 taxa) GO:0036440, IDA, PMID:7626013 (PseudoCAP) SOUND (gene identity inferred) Purified CSII matches PrpC (dimer, ~41-kDa subunit) and purified recombinant PrpC has CS activity (PMID:36377867, full text). The 1995 paper does not identify the gene, so a SUSPECTED CHECK defect asks PseudoCAP to add/repoint to PMID:36377867. E. coli PrpC (P31660), S. typhimurium PrpC (Q56063), yeast CIT1/CIT2/CIT3, S. pombe cit1, human/mouse/rat CS, Arabidopsis CSY4, Drosophila kdn, Dictyostelium and others Yes; dozens of experimentally characterised citrate synthases. No GO_CENTRAL defect.
PTN000201223 GO:0006099 tricarboxylic acid cycle 4 270 (123 taxa) GO:0006099, IDA, PMID:7626013 (PseudoCAP) SOUND in substance (gene identity inferred; participation conditional) PrpC supplies citrate in vivo when GltA is absent (ΔgltA ΔprpC not obtainable), so it can take part in the TCA cycle, but GltA is the TCA-cycle enzyme in wild type. The same CHECK defect applies. yeast CIT1 (S000005284), CIT3 (S000006205), S. pombe cit1 (SPAC6C3.04) Yes, on the mitochondrial citrate synthases. The term is right for the eukaryotic CS members; for the bacterial PrpC subclade it is a backup role. Not filed as a GO_CENTRAL defect (raised as a question).

Annotation decisions