PrpC (PA0795) is the 2-methylcitrate synthase of Pseudomonas aeruginosa, the first enzyme of the 2-methylcitrate cycle that converts propionyl-CoA and oxaloacetate to 2-methylcitrate during propionate catabolism. It is a cytoplasmic homodimer of about 41-kDa subunits of the citrate synthase fold, whose structure has been solved with and without bound oxaloacetate. The purified enzyme is promiscuous, condensing acetyl-CoA with oxaloacetate to citrate at rates comparable to its 2-methylcitrate synthase activity. A prpC deletion cannot grow on propionate. prpC lies in the PrpR-repressed prp operon; basal PrpC expression rescues a mutant lacking the TCA-cycle citrate synthase GltA, and gltA mutants are selected for mutations that derepress prpC.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro 2-methylcitrate/citrate synthase type II mapping. Reason: PrpC is a soluble metabolic enzyme with no signal peptide or TM segment; purified as a soluble homodimer. Cytoplasm is as precise as warranted. Supporting Evidence: PMID:36377867 PrpCPa is a homodimer. |
| GO:0005975 carbohydrate metabolic process | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN000201223 seeded by human citrate synthase (O75390) alone. Reason: PrpC acts in propionate catabolism and, as a backup, in citrate formation; neither is carbohydrate metabolism, and GO:0006099 is not under GO:0005975. The row adds a vague process with no support specific to this gene. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000201223 Β· PTN000201223 SUPPORTS SOURCE BUT NOT TARGET Single-seed IBD (human CS) of a broad process on a node that also holds the bacterial PrpC subclade, whose substrate is propionyl-CoA. UniProtKB:O75390 Β· human CS (sole seed) SUPPORTS SOURCE BUT NOT TARGET Mitochondrial TCA-cycle citrate synthase; its process does not transfer to a 2-methylcitrate synthase. Supporting Evidence: PMID:36377867 The 2-methylcitrate synthase mutant (ΞprpC) was unable to grow on propionate as a sole carbon source but displayed no detectable growth deficit on any of the other tested carbon sources. |
| GO:0006099 tricarboxylic acid cycle | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from the 4-seed TCA-cycle IBD at PTN000201223 (yeast CIT1, CIT3, S. pombe cit1 and this gene). The IBD stands on the yeast seeds. Reason: PrpC can feed citrate into the TCA cycle, enough to keep a gltA mutant alive, and a gltA prpC double mutant could not be made; but GltA is the TCA-cycle citrate synthase in wild type, so this is a conditional, non-core role. Supporting Evidence: PMID:36377867 In the absence of citrate synthase (GltA), Pa can survive because of the low-level basal expression of PrpC, a promiscuous enzyme that also has citrate synthase activity. PMID:36377867 Consistent with this, and despite repeated attempts at doing so, we were unable to make a ΞgltA ΞprpC double mutant. |
| GO:0006099 tricarboxylic acid cycle | IDA PMID:7626013 Purification and characterization of citrate synthase isoenz... | KEEP AS NON CORE | Summary: PseudoCAP IDA, seed of the PTN000201223 TCA-cycle IBD. The 1995 paper purified two native citrate synthases without identifying their genes. Reason: Seed verdict SOUND in substance. The dimeric CSII matches PrpC, and PrpC's in vivo contribution to citrate supply is shown in PMID:36377867, but participation is a backup role and the 1995 paper cannot itself tie CSII to PA0795 (see source_defects). Supporting Evidence: PMID:7626013 Chemical cross-linking of the native enzymes with either dimethyl suberimidate or glutaraldehyde followed by electrophoretic analysis by SDS/PAGE showed that CSI is a hexamer and CSII is a dimer. PMID:36377867 In the absence of citrate synthase (GltA), Pa can survive because of the low-level basal expression of PrpC, a promiscuous enzyme that also has citrate synthase activity. |
| GO:0006099 tricarboxylic acid cycle | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: InterPro bacterial-type citrate synthase / UniPathway mapping. Reason: Same conditional role as the IBA and IDA rows. Supporting Evidence: PMID:36377867 In the absence of citrate synthase (GltA), Pa can survive because of the low-level basal expression of PrpC, a promiscuous enzyme that also has citrate synthase activity. |
| GO:0019543 propionate catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PrpC subclade node PTN002621568 (E. coli and Salmonella PrpC). Reason: Core process; PrpC catalyses the first step of the 2-methylcitrate cycle and a prpC deletion cannot grow on propionate. Supporting Evidence: PMID:36377867 The 2-methylcitrate synthase mutant (ΞprpC) was unable to grow on propionate as a sole carbon source but displayed no detectable growth deficit on any of the other tested carbon sources. |
| GO:0036440 citrate synthase activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from the 19-seed PTN000201223 IBD; this gene is among its own sources because of its PseudoCAP IDA row, which is expected. Reason: True: purified PrpC condenses acetyl-CoA with oxaloacetate at rates comparable to its 2-methylcitrate synthase activity, and it supports growth without GltA. It is a genuine secondary activity; the core activity is 2-methylcitrate synthase. The IBD rests on many characterised citrate synthases and on E. coli and Salmonella PrpC. Supporting Evidence: PMID:36377867 Purified PrpCPa exhibits both citrate synthase activity (with acetyl-CoA as a substrate) and 2-methylcitrate synthase activity (with propionyl-CoA as a substrate). |
| GO:0036440 citrate synthase activity | IDA PMID:7626013 Purification and characterization of citrate synthase isoenz... | KEEP AS NON CORE | Summary: PseudoCAP IDA and one of 19 seeds of PTN000201223. The cited paper purified native CSI and CSII without naming genes. Reason: Seed verdict SOUND (gene identity inferred). CSII matches PrpC and purified recombinant PrpC has citrate synthase activity, so the claim is true; it is a secondary activity. The reference problem is recorded on the TCA-cycle IDA row, which shares it. Supporting Evidence: PMID:36377867 Purified PrpCPa exhibits both citrate synthase activity (with acetyl-CoA as a substrate) and 2-methylcitrate synthase activity (with propionyl-CoA as a substrate). PMID:36377867 PrpCPa is a homodimer. |
| GO:0036440 citrate synthase activity | IEA GO_REF:0000003 | KEEP AS NON CORE | Summary: EC 2.3.3.1/2.3.3.16 mapping. Reason: Same secondary activity as the IBA and IDA rows. Supporting Evidence: PMID:36377867 Purified PrpCPa exhibits both citrate synthase activity (with acetyl-CoA as a substrate) and 2-methylcitrate synthase activity (with propionyl-CoA as a substrate). |
| GO:0046912 acyltransferase activity, acyl groups converted into alkyl on transfer | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro citrate synthase family mapping to the parent class. Reason: True but uninformative; GO:0050440 2-methylcitrate synthase activity, accepted here, is_a GO:0046912. |
| GO:0050440 2-methylcitrate synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PrpC subclade node PTN002621568. Reason: Core activity, shown directly with purified PrpC. Supporting Evidence: PMID:36377867 Purified PrpCPa exhibits both citrate synthase activity (with acetyl-CoA as a substrate) and 2-methylcitrate synthase activity (with propionyl-CoA as a substrate). |
| GO:0050440 2-methylcitrate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: ARBA/EC 2.3.3.5 mapping. Reason: Same claim as the IBA row, with direct biochemical support. Supporting Evidence: PMID:36377867 Purified PrpCPa exhibits both citrate synthase activity (with acetyl-CoA as a substrate) and 2-methylcitrate synthase activity (with propionyl-CoA as a substrate). |
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Download this section (compressed HTML)Q: The PTN000201223 TCA-cycle IBD (seeded by yeast CIT1/CIT3 and S. pombe cit1) propagates to the bacterial PrpC subclade, whose members are mainly 2-methylcitrate synthases beside a dedicated GltA. Should the TCA-cycle term be placed on a node that excludes the PrpC subclade?
Experiment: Quantify the share of cellular citrate synthase flux carried by PrpC in wild-type P. aeruginosa on propionate-containing media (13C tracing in gltA+ and prpC strains).
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