ArcB (PA5172) is the catabolic ornithine carbamoyltransferase of Pseudomonas aeruginosa, the second enzyme of the arginine deiminase (ADI) pathway encoded by the arcDABC operon. It catalyses the phosphorolysis of L-citrulline to L-ornithine and carbamoyl phosphate, which carbamate kinase (ArcC) then uses to make ATP, supporting anaerobic growth on arginine. Unlike the anabolic OTC (ArgF), ArcB has poor affinity and marked cooperativity for carbamoyl phosphate and does not run the biosynthetic reaction physiologically. It is a cytoplasmic dodecamer (tetramer of trimers), allosterically activated by phosphate and nucleoside monophosphates and inhibited by polyamines; expression is induced by arginine under oxygen limitation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004585 ornithine carbamoyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN000150424 IBD (9 seeds, including human, rat, yeast, fission yeast, E. coli and M. tuberculosis OTCs, and arcB itself, which is expected, not circular). Reason: Core MF; the IBD stands on eight characterised OTCs without this seed. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt Catalyzes the phosphorolysis of citrulline, the reverse reaction of the biosynthetic one, yielding ornithine and carbamoyl phosphate which serve to generate ATP from ADP |
| GO:0004585 ornithine carbamoyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC/Rhea/UniRule mapping. Reason: Correct; agrees with the curated function. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt Catalyzes the phosphorolysis of citrulline, the reverse reaction of the biosynthetic one, yielding ornithine and carbamoyl phosphate which serve to generate ATP from ADP |
| GO:0004585 ornithine carbamoyltransferase activity | IMP PMID:6438064 Pseudomonas aeruginosa mutants affected in anaerobic growth ... | ACCEPT | Summary: PseudoCAP IMP and one of nine seeds of the PTN000150424 GO:0004585 IBD. arcB mutants lack catabolic OTC activity. Seed verdict SOUND. Reason: Loss of an activity in a mutant does not by itself show that the gene encodes it, but arcB was subsequently confirmed as the structural gene of the catabolic OTC, so the term is correct for this gene. Supporting Evidence: PMID:6438064 All mutants (except one) were defective in at least one of the three enzymes of the arginine deiminase pathway (arcA, arcB, and arcC mutants) file:PSEAE/arcB/arcB-uniprot.txt Catalyzes the phosphorolysis of citrulline, the reverse reaction of the biosynthetic one, yielding ornithine and carbamoyl phosphate which serve to generate ATP from ADP |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: UniProt subcellular location mapping. Reason: A soluble dodecameric enzyme of a cytoplasmic catabolic pathway. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}. |
| GO:0006520 amino acid metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the aspartate/ornithine carbamoyltransferase domains. Reason: Correct but general; ArcB acts in arginine catabolism by the ADI pathway, so GO:0006527 L-arginine catabolic process is the supported specific term (as used for arcA). Proposed replacements: L-arginine catabolic process Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt DISRUPTION PHENOTYPE: Cells lacking this gene are blocked in the arginine deiminase pathway. |
| GO:0006526 L-arginine biosynthetic process | IBA GO_REF:0000033 | REMOVE | Summary: IBA from the PTN000150424 IBD of GO:0006526, seeded by anabolic OTCs (yeast and fission yeast Arg3, A. fumigatus Q4WNW5, M. tuberculosis ArgF). arcB is not a seed. Reason: ArcB is the catabolic OTC: it runs the citrulline-consuming direction in the ADI pathway and, because of poor affinity and cooperativity for carbamoyl phosphate, does not carry out the biosynthetic reaction. P. aeruginosa has a separate anabolic OTC (ArgF). The biosynthetic process was inherited from the node but lost in this catabolic paralog. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000150424 · PTN000150424 SUPPORTS SOURCE BUT NOT TARGET OTC family node (157 leaf IBAs, 119 taxa) that includes both anabolic OTCs (ArgF, ArgI, Arg3, human OTC) and catabolic ADI-pathway OTCs (ArcB). The MF IBD is right for all; the arginine and citrulline biosynthesis IBDs are right only for the anabolic members. SGD:S000003624 · ARG3 (yeast) SUPPORTS SOURCE BUT NOT TARGET Anabolic OTC; its biosynthetic role does not transfer to catabolic ArcB. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt This catabolic OTCase does not carry out the biosynthetic reaction because of a poor affinity and a marked cooperativity for carbamoyl phosphate |
| GO:0006526 L-arginine biosynthetic process | IEA GO_REF:0000104 | REMOVE | Summary: UniRule (HAMAP OTC rule) transfer of arginine biosynthesis. Reason: Wrong for the catabolic OTC, which does not carry out the biosynthetic reaction; the family rule does not separate anabolic from catabolic OTCs. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt This catabolic OTCase does not carry out the biosynthetic reaction because of a poor affinity and a marked cooperativity for carbamoyl phosphate |
| GO:0006591 ornithine metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the OTC signature. Reason: True in that ArcB produces ornithine, but ornithine is a by-product of the ADI pathway, whose purpose is ATP generation from arginine. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt Catalyzes the phosphorolysis of citrulline, the reverse reaction of the biosynthetic one, yielding ornithine and carbamoyl phosphate which serve to generate ATP from ADP |
| GO:0016597 amino acid binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the carbamoyltransferase amino-acid-binding domain. Reason: True (ornithine/citrulline binding by the substrate-binding domain) but a facet of the catalytic activity. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt IPR006131; Asp_carbamoyltransf_Asp/Orn-bd |
| GO:0016743 carboxyl- or carbamoyltransferase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO mapping. Reason: GO:0004585 ornithine carbamoyltransferase activity, accepted in this review, is_a GO:0016743. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt Catalyzes the phosphorolysis of citrulline, the reverse reaction of the biosynthetic one, yielding ornithine and carbamoyl phosphate which serve to generate ATP from ADP |
| GO:0019240 citrulline biosynthetic process | IBA GO_REF:0000033 | REMOVE | Summary: IBA from the PTN000150424 IBD of GO:0019240, seeded by anabolic OTCs (rat and human OTC, E. coli ArgI and ArgF). arcB is not a seed. Reason: ArcB consumes citrulline (phosphorolysis to ornithine and carbamoyl phosphate); it does not synthesise it. The GO_CENTRAL defect covering this IBD and the GO:0006526 IBD is recorded on the GO:0006526 IBA row. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000150424 · PTN000150424 SUPPORTS SOURCE BUT NOT TARGET Citrulline biosynthesis holds for the anabolic OTCs that seed it but not for the catabolic ADI-pathway OTC; see the GO:0006526 row for the node-level defect. UniProtKB:P00480 · human OTC SUPPORTS SOURCE BUT NOT TARGET Urea-cycle OTC that synthesises citrulline; does not transfer to catabolic ArcB. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt This catabolic OTCase does not carry out the biosynthetic reaction because of a poor affinity and a marked cooperativity for carbamoyl phosphate file:PSEAE/arcB/arcB-uniprot.txt Catalyzes the phosphorolysis of citrulline, the reverse reaction of the biosynthetic one, yielding ornithine and carbamoyl phosphate which serve to generate ATP from ADP |
| GO:0006527 L-arginine catabolic process | IC file:PSEAE/arcB/arcB-notes.md | NEW | Summary: Proposed process annotation. ArcB catalyses step 2 of the arginine deiminase pathway, and arcB mutants cannot grow by anaerobic arginine catabolism. Reason: The enzyme performs a step of arginine catabolism, so it participates in the process (not merely required for it). Same term as used for arcA; GO has no ADI-specific child. Supporting Evidence: file:PSEAE/arcB/arcB-uniprot.txt DISRUPTION PHENOTYPE: Cells lacking this gene are blocked in the arginine deiminase pathway. PMID:6438064 All mutants (except one) were defective in at least one of the three enzymes of the arginine deiminase pathway (arcA, arcB, and arcC mutants) |
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Download this section (compressed HTML)Q: Should GO have a process term for the arginine deiminase pathway (arginine fermentation to ornithine with ATP generation), as a child of L-arginine catabolic process?
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