ArcC (PA5173) is the carbamate kinase of Pseudomonas aeruginosa, the third enzyme of the arginine deiminase (ADI) pathway encoded by the arcDABC operon. It transfers the phosphate of carbamoyl phosphate, produced from citrulline by the catabolic ornithine carbamoyltransferase ArcB, to ADP, forming ATP, ammonia and carbon dioxide. This substrate-level phosphorylation lets the bacterium grow anaerobically on arginine when oxygen and nitrate are scarce, and aerobically the enzyme serves as a source of ammonia. ArcC is a cytoplasmic homodimer, distinct from carbamoyl-phosphate synthetase and acetate kinase, inhibited by ATP (avoiding a futile cycle with carbamoyl-phosphate synthetase), and induced by anaerobiosis and arginine and repressed by ammonia.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000256 allantoin catabolic process | IBA GO_REF:0000033 | REMOVE | Summary: IBA from the PTN000764469 IBD of GO:0000256, seeded only by E. coli AllK (P37306), the carbamate kinase of anaerobic allantoin assimilation. arcC is not a seed of this term. Reason: ArcC is the carbamate kinase of the arginine deiminase pathway: it is encoded in the arc operon, induced by arginine and anaerobiosis, and arcC mutants are blocked in anaerobic arginine catabolism. Carbamate kinases are shared terminal enzymes of several carbamoyl-phosphate-producing catabolic pathways, and the pathway each paralog serves is set by its operon, not inherited with the fold. Nothing links P. aeruginosa ArcC to allantoin degradation. Same kind of pathway-specific over-propagation as the biosynthetic IBAs removed from arcB. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE WRONG ORTHOLOG OR PARALOG Sources checked: PANTHER:PTN000764469 · PTN000764469 SUPPORTS SOURCE BUT NOT TARGET Carbamate kinase node (7 leaves, 6 taxa) containing allantoin-pathway AllK and ADI-pathway kinases (P. aeruginosa ArcC, H. influenzae ArcC P44769, Salmonella STM4466, Geobacter CpkA). The MF IBD is right for all; the allantoin process IBD only for AllK. UniProtKB:P37306 · allK (E. coli) SUPPORTS SOURCE BUT NOT TARGET IDA allantoin catabolism (PMID:36384810) for AllK; does not transfer to ADI-pathway ArcC. Supporting Evidence: file:PSEAE/arcC/arcC-uniprot.txt PATHWAY: Amino-acid degradation; L-arginine degradation via ADI pathway. PMID:6438064 The mutations arcA (arginine deiminase), arcB (catabolic ornithine carbamoyltransferase), arcC (carbamate kinase), and arcD were highly cotransducible file:PSEAE/arcC/arcC-notes.md the PTN000764469 IBD of GO:0000256 allantoin catabolic process rests on E. coli AllK alone |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | TOO GENERAL | Summary: UniProt subcellular location mapping. Reason: True for this soluble enzyme, but GO:0005829 cytosol, accepted in this review from the IBA, is part_of cytoplasm. Supporting Evidence: file:PSEAE/arcC/arcC-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN001252214 IBD of cytosol, seeded by E. coli YahI (P77624; IDA, EcoCyc). Reason: A soluble dimeric kinase of a cytoplasmic catabolic pathway with no signal peptide or transmembrane segment; cytosol is the expected location and the node seed is direct. Supporting Evidence: file:PSEAE/arcC/arcC-uniprot.txt SUBUNIT: Homodimer. {ECO:0000269|PubMed:6286599}. |
| GO:0006525 arginine metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the carbamate kinase signature. Reason: Correct but general. ArcC acts in arginine catabolism by the ADI pathway, so GO:0006527 L-arginine catabolic process (is_a arginine metabolic process) is the supported term, as used for arcA and arcB. GO:0019546 L-arginine deiminase pathway is obsolete. Proposed replacements: L-arginine catabolic process Supporting Evidence: file:PSEAE/arcC/arcC-uniprot.txt PATHWAY: Amino-acid degradation; L-arginine degradation via ADI pathway. PMID:6438064 The mutations arcA (arginine deiminase), arcB (catabolic ornithine carbamoyltransferase), arcC (carbamate kinase), and arcD were highly cotransducible |
| GO:0008804 carbamate kinase activity | EXP PMID:6286599 Carbamate kinase from Pseudomonas aeruginosa: purification, ... | ACCEPT | Summary: Purified PAO1 carbamate kinase, with kinetics and regulation. Reason: Core MF, directly assayed on the purified enzyme. Supporting Evidence: PMID:6286599 Pseudomonas aeruginosa PAO1 possessed a carbamate kinase (CKase) distinct from carbamoylphosphate synthetase as well as from a constitutive acetate kinase which also catalyzes the phosphorylation of ADP by carbamoylphosphate file:PSEAE/arcC/arcC-uniprot.txt Catalyzes the phosphorylation of ADP by carbamoyl phosphate (PubMed:6286599) |
| GO:0008804 carbamate kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN000764469 IBD, seeded by arcC itself (PseudoCAP IMP; expected, not circular) and E. coli AllK (IDA). Reason: Core MF; the IBD stands on AllK without this seed, and the node term suits a clade of carbamate kinases. Supporting Evidence: file:PSEAE/arcC/arcC-uniprot.txt Catalyzes the phosphorylation of ADP by carbamoyl phosphate (PubMed:6286599) |
| GO:0008804 carbamate kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC/Rhea/InterPro mapping. Reason: Correct; agrees with the purified-enzyme activity. Supporting Evidence: file:PSEAE/arcC/arcC-uniprot.txt Catalyzes the phosphorylation of ADP by carbamoyl phosphate (PubMed:6286599) |
| GO:0008804 carbamate kinase activity | IMP PMID:6438064 Pseudomonas aeruginosa mutants affected in anaerobic growth ... | ACCEPT | Summary: PseudoCAP IMP; seed of the PTN001252214 (kinase activity) and PTN000764469 (carbamate kinase activity) IBDs. arcC mutants lack carbamate kinase. Seed verdict SOUND. Reason: Loss of an activity in a mutant does not alone show that the gene encodes it, but arcC was later confirmed as the structural gene (sequence, purified enzyme, crystal structure 8CRV), so the term is correct for this gene. Supporting Evidence: PMID:6438064 The mutations arcA (arginine deiminase), arcB (catabolic ornithine carbamoyltransferase), arcC (carbamate kinase), and arcD were highly cotransducible file:PSEAE/arcC/arcC-uniprot.txt Catalyzes the phosphorylation of ADP by carbamoyl phosphate (PubMed:6286599) |
| GO:0006527 L-arginine catabolic process | IC file:PSEAE/arcC/arcC-notes.md | NEW | Summary: Proposed process annotation. ArcC catalyses the ATP-yielding last step of the arginine deiminase pathway, and arcC mutants cannot grow by anaerobic arginine catabolism. Reason: The enzyme performs a step of arginine catabolism, so it participates in the process. Same term as used for arcA and arcB; GO has no current ADI-specific child. Supporting Evidence: file:PSEAE/arcC/arcC-uniprot.txt PATHWAY: Amino-acid degradation; L-arginine degradation via ADI pathway. PMID:6438064 The mutations arcA (arginine deiminase), arcB (catabolic ornithine carbamoyltransferase), arcC (carbamate kinase), and arcD were highly cotransducible |
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Download this section (compressed HTML)Q: Should GO restore a process term for the arginine deiminase pathway (arginine fermentation to ornithine with ATP generation) as a child of L-arginine catabolic process, so that ADI-pathway carbamate kinases can be distinguished from allantoin- and other-pathway carbamate kinases?
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