lysA-II (PP_5227) encodes the PLP-dependent diaminopimelate decarboxylase (DAPDC; EC 4.1.1.20) that converts meso-2,6-diaminopimelate to L-lysine and carbon dioxide in the terminal reaction of the diaminopimelate pathway. KT2440 also encodes the closely related LysA-I protein, and the relative physiological contributions of the two paralogs are unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This root catalytic term is redundant with the specific DAPDC activity. Reason: GO:0008836 identifies the actual substrate-specific reaction. |
| GO:0008836 diaminopimelate decarboxylase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the defining LysA-II molecular function. Reason: EC 4.1.1.20, RHEA:15101, HAMAP MF_02120, NCBIfam:TIGR01048, and the LysA-specific InterPro signature support the same decarboxylation. Supporting Evidence: file:PSEPK/lysA/lysA-uniprot.txt Full=Diaminopimelate decarboxylase file:PSEPK/lysA/lysA-deep-research-openscientist.md The core functional assignment is that Q88CF4 is a **DAPDC (EC 4.1.1.20)** catalyzing: |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: PLP binding is valid cofactor context for DAPDC catalysis. Reason: UniProt and the class-II decarboxylase family support PLP dependence, but cofactor binding is less informative than the substrate-specific reaction. |
| GO:0009085 L-lysine biosynthetic process | IEA file:PSEPK/lysA/lysA-uniprot.txt | NEW | Summary: LysA-II performs the terminal reaction of L-lysine biosynthesis. Reason: LysA-II catalyzes the terminal decarboxylation of meso-2,6-diaminopimelate to L-lysine, the final step of the diaminopimelate (DAP) route of lysine biosynthesis. UniProt cross-references Q88CF4 to the DAP-route process term GO:0009089 via IEA:UniProtKB-UniRule; GO:0009085 (L-lysine biosynthetic process) is used here to capture this terminal DAP-pathway biology. Supporting Evidence: file:PSEPK/lysA/lysA-uniprot.txt GO:0009089; P:L-lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule file:PSEPK/lysA/lysA-uniprot.txt L-lysine biosynthesis via DAP |
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Gap: The relative in-vivo flux, conditional expression, and redundancy of the Q88CF4 LysA-II and Q88L58 LysA-I paralogs are unresolved.
BIOLOGY
What is known: Both proteins retain the exact DAP decarboxylase assignment; adjacency of Q88CF4 to dapF is context, not proof that it is the dominant copy.
Provenance (the field's own admissions):
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