Bacterial succinylarginine catabolism to glutamate and succinate

A five-reaction bacterial pathway that transfers a succinyl group from succinyl-CoA to L-arginine, hydrolyzes the guanidino group, transaminates the resulting N-succinyl-L-ornithine, oxidizes the semialdehyde, and removes the succinyl group to produce L-glutamate and succinate. The initiating transferase may be a single-chain enzyme or a two-chain complex. Arginine transport, regulation, alternative arginine-catabolic routes, and downstream central metabolism are outside the module boundary.

The module is species-neutral: the AST pathway is shared by enterobacteria (Escherichia coli K-12 astCADBE, the best-characterized implementation) and pseudomonads (P. aeruginosa aruCFGDB-aruE, P. putida KT2440), and the PANTHER, NCBIfam and HAMAP families for each step span Proteobacteria (Pseudomonadota), the taxonomic context used here. KT2440 proteins are kept as one exemplar; E. coli and P. aeruginosa members were added because they carry the experimental evidence. Every grounded accession has a COMPLETE gene review. Step 1 varies in architecture: a single chain (E. coli AstA) or a heterotetramer of two paralogous chains (AruF/AruG; KT2440 AstA-II/AstA-I). InterPro IPR017651 and IPR017650, corroborated by NCBIfam TIGR03245 and TIGR03244, distinguish the alpha-like and beta-like chains; PANTHER PTHR30420:SF1 groups both chain types with single-chain AstA and so does not discriminate the architecture. PTHR30420 groups the AstA transferases (SF1) with the AstB dihydrolases (SF2) although their catalytic domains differ (Pfam AstA versus AstB); the PTHR30420 family review finds the GO:0009015 dihydrolase IBD at PTN000764516 TOO_DEEP, because it propagates to SF1 transferases, so that node is deliberately not used as an AstB ancestral node, and the AstB step is grounded at SF2. The AstE step uses PTHR15162:SF7; 18 cyanobacterial SF7 members named probable aspartoacylases are recorded as exceptions to the AstE activity in the PTHR15162 family review. The AstD selector uses broad PTHR11699 because the Q88EI4 and P76217 records have no populated PANTHER subfamily; its ancestral node grounds only the generic aldehyde dehydrogenase chemistry. The module validator's FAMILY_FUNCTION_UNREVIEWED warning on that step is expected: the PTHR11699 family review truthfully leaves the generic GO:0004029 scope UNRESOLVED across ~47 subfamilies, and the verified family id is kept because it records membership. PTN002279553 (P59319) and PTN002309601 (Q88EI7) are TreeGrafter sources of broad PLP/self-binding and amide-hydrolase rows and are not used as ancestral nodes. The KT2440 AstC assignment of PP_4481 (annotated by UniProt as ArgD) rests on operon context and SF113 membership.