dapE encodes the metallodependent succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) that hydrolyzes N-succinyl-LL-diaminopimelate to LL-diaminopimelate and succinate in the succinylated route of L-lysine biosynthesis. Its proteobacterial DapE-specific family distinguishes it from related ArgE acetylornithine deacetylases.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006526 L-arginine biosynthetic process | IEA GO_REF:0000118 | REMOVE | Summary: This TreeGrafter process call reflects related ArgE enzymes, not PSEPK DapE. Reason: Q88MP5 has the DapE-specific reaction, pathway assignment, and NCBIfam:TIGR01246 signature. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Zinc binding is valid catalytic-metal context for DapE. Reason: The metallohydrolase annotation supports metal binding, which is secondary to substrate-specific catalysis. |
| GO:0008777 acetylornithine deacetylase activity | IEA GO_REF:0000118 | REMOVE | Summary: This activity belongs to related ArgE-family proteins. Reason: Q88MP5 is assigned to the proteobacterial DapE subfamily and EC 3.5.1.18; no evidence supports acetylornithine as its physiological substrate. |
| GO:0009014 succinyl-diaminopimelate desuccinylase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the defining DapE molecular function. Reason: EC 3.5.1.18, HAMAP MF_01690, and NCBIfam:TIGR01246 support the same reaction. Support is the curated HAMAP rule's FUNCTION statement and the DapE family classifications (a rule-based, not experimental, assignment for Q88MP5). Supporting Evidence: file:PSEPK/dapE/dapE-uniprot.txt Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminopimelate (DAP) file:PSEPK/dapE/dapE-uniprot.txt HAMAP; MF_01690; DapE; 1. file:PSEPK/dapE/dapE-uniprot.txt NCBIfam; TIGR01246; dapE_proteo; 1. |
| GO:0009085 L-lysine biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: DapE deprotects LL-diaminopimelate in L-lysine biosynthesis. Reason: UniProt assigns Q88MP5 to L-lysine biosynthesis via the DAP pathway. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: This generic hydrolase term is redundant with the specific DapE activity. Reason: GO:0009014 captures the substrate-specific reaction. |
| GO:0050897 cobalt ion binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: Cobalt binding is plausible catalytic-metal context for DapE. Reason: UniProt records cobalt for this metallohydrolase, but metal binding is secondary to catalysis. |
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