arcA (PA5171) encodes arginine deiminase (ADI, EC 3.5.3.6) of Pseudomonas aeruginosa, a cytoplasmic homotetrameric enzyme of the pentein (guanidino-group modifying enzyme) fold that hydrolyses L-arginine to L-citrulline and ammonia through a covalent S-alkylthiouronium intermediate on the active-site Cys406. It is the first enzyme of the arginine deiminase pathway, encoded with the arginine:ornithine antiporter ArcD, catabolic ornithine carbamoyltransferase ArcB and carbamate kinase ArcC in the arcDABC operon, which is induced by oxygen limitation. The pathway converts arginine to ornithine, ammonia and CO2 and yields ATP by substrate-level phosphorylation, which lets P. aeruginosa grow slowly by arginine fermentation when oxygen and nitrate are absent. The enzyme is activated by Mg2+ or Mn2+, inhibited by Zn2+, and has been characterised kinetically and by several crystal structures.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/UniProt subcellular-location mapping to cytoplasm. ADI has no signal peptide or transmembrane segment. Reason: ADI acts on arginine imported by ArcD and feeds intracellular catabolic ornithine carbamoyltransferase and carbamate kinase, so the core activity is cytoplasmic. The location is inferred, but consistent with a soluble tetrameric enzyme purified from cell extracts. Supporting Evidence: file:PSEAE/arcA/arcA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}. PMID:2537202 The native arginine deiminase had an estimated molecular mass of 175-180 kDa, suggesting a tetrametric structure. |
| GO:0006527 L-arginine catabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/InterPro (ADI family) mapping to L-arginine catabolic process. Reason: ADI catalyses the first step of the arginine deiminase pathway, so the enzyme itself does part of the work of arginine catabolism. Genetic evidence in PAO1 shows arcA mutants cannot grow by anaerobic arginine catabolism. GO has no more specific term for the ADI route, so this is the appropriate level. 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) PMID:14701825 ADI is involved in the first step of the most widespread anaerobic route of arginine degradation. |
| GO:0016990 arginine deiminase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PAINT node PTN005338738, which spans the PTHR47271 arginine deiminase family (bacteria, archaea, protists). Its IBD is seeded only by this gene's own PseudoCAP IMP row; the target appearing in its own WITH/FROM is expected, not circular. Reason: PA5171 is the canonical, experimentally characterised P. aeruginosa ADI (purified enzyme, kinetics, crystal structures, Cys406 mechanism), so it is inside the clade whose function this is and the seed is sound. The node is broad, a SPECIATION event placed at LUCA spanning the whole PTHR47271 family, and after checking the tree (2026-11-05) only one small clade looks like an over-propagation: the Korarchaeum cryptofilum pair PTN008230056, whose members are named for other pentein activities. That concerns other leaves, not this gene, and is flagged for checking. Supporting Evidence: PMID:2537202 The N-terminal amino acid sequence of arginine deiminase was in agreement with the corresponding nucleotide sequence. PMID:16091358 The function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. |
| GO:0016990 arginine deiminase activity | IEA GO_REF:0000120 | ACCEPT | Summary: HAMAP/InterPro/EC/Rhea-based arginine deiminase activity. Reason: Same correct core claim as the IBA and IMP rows, from the curated ADI family rule. Supporting Evidence: file:PSEAE/arcA/arcA-uniprot.txt Reaction=L-arginine + H2O = L-citrulline + NH4(+); file:PSEAE/arcA/arcA-uniprot.txt Belongs to the arginine deiminase family. |
| GO:0016990 arginine deiminase activity | IMP PMID:6438064 Pseudomonas aeruginosa mutants affected in anaerobic growth ... | ACCEPT | Summary: PseudoCAP IMP; sole seed of the PTN005338738 arginine deiminase activity IBD (23 leaf IBAs, 18 taxa). Vander Wauven et al. (1984) isolated PAO mutants unable to grow anaerobically on arginine and classified them by which ADI-pathway enzyme they lacked; arcA mutants lack arginine deiminase. Reason: A mutant phenotype can support a molecular function when the mutant is shown to lack that specific enzyme activity and the mutation lies in the structural gene. Both hold here. The arcA class was defined by loss of ADI activity alone, distinct from the regulatory class that lost all three enzymes, and the arcA locus was then shown to encode the ADI polypeptide (PMID:2537202). This is not the indirect-phenotype failure (loss of growth or of an unrelated downstream activity). Direct biochemical evidence (purified enzyme, kinetics, structures) would justify an IDA from PMID:2537202, but the IMP is sound as it stands. Supporting Evidence: PMID:6438064 The mutations arcA (arginine deiminase), arcB (catabolic ornithine carbamoyltransferase), arcC (carbamate kinase), and arcD were highly cotransducible and mapped in the 17-min chromosome region. PMID:6438064 Some mutations in the arc cluster led to low, noninducible levels of all three arginine deiminase pathway enzymes PMID:2537202 The arcA open reading frame specifies a polypeptide of 46.3 kDa. The same molecular mass was obtained for the subunit of purified arginine deiminase after electrophoresis under denaturing conditions. |
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Download this section (compressed HTML)Q: Does the Korarchaeum cryptofilum pair under PTN005338738 (PTN008230056; B1L3J0, named an N-dimethylarginine dimethylaminohydrolase, and B1L477, an amidinotransferase) have arginine deiminase activity, or should the ADI IBD be blocked there? These are the only leaves of the node whose names point to a different pentein activity; B. subtilis YkgA and the archaeal Q8TSK4 and Q97TX4, flagged earlier on length, sit beside genuine ArcA enzymes in the tree.
Q: Should the PseudoCAP seed for PTN005338738 be supplemented by an IDA from the purified-enzyme study (PMID:2537202), which ties the activity to the arcA product directly?
Experiment: Express and purify the Korarchaeum cryptofilum PTHR47271 pair (B1L3J0, B1L477) and B. subtilis YkgA and assay arginine deiminase versus dimethylarginine dimethylaminohydrolase activity, to settle whether the ADI node term applies to them.
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