DdlA is a cytoplasmic ATP-dependent D-alanine-D-alanine ligase. It joins two D-alanine molecules to form the D-Ala-D-Ala dipeptide used by MurF during peptidoglycan stem-peptide precursor assembly. Q88EV6 is the DdlA-like member of a multi-paralog ligase family in KT2440.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binding is required for catalysis but is not the defining function. Reason: The ATP-grasp domain and annotated ATP-binding region support this cofactor property. Supporting Evidence: file:PSEPK/ddlA/ddlA-uniprot.txt /note="ATP-grasp" |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Cytoplasm is the appropriate compartment for precursor ligation. Reason: The reviewed UniProt record assigns Q88EV6 to the cytoplasm. Supporting Evidence: file:PSEPK/ddlA/ddlA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005829 cytosol | IEA GO_REF:0000118 | MARK AS OVER ANNOTATED | Summary: This is redundant with the accepted bacterial cytoplasm annotation. Reason: Retain GO:0005737 as the single informative cellular-component annotation. |
| GO:0008716 D-alanine-D-alanine ligase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the exact reaction assigned by convergent curated rules and signatures. Reason: HAMAP, Rhea, EC, PROSITE, TIGRFAM, and PANTHER support DdlA chemistry. Supporting Evidence: file:PSEPK/ddlA/ddlA-uniprot.txt RecName: Full=D-alanine--D-alanine ligase A |
| GO:0009252 peptidoglycan biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Peptidoglycan precursor assembly is the direct process context. Reason: D-Ala-D-Ala is the dipeptide substrate supplied to MurF. Supporting Evidence: file:PSEPK/ddlA/ddlA-uniprot.txt Cell wall biogenesis; peptidoglycan biosynthesis. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Divalent-metal binding supports catalysis but is not the core function. Reason: UniProt records two magnesium or manganese ions per subunit. Supporting Evidence: file:PSEPK/ddlA/ddlA-uniprot.txt Binds 2 magnesium or manganese ions per subunit. |
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Download this section (compressed HTML)Q: How redundant are DdlA and DdlB-family paralogs across growth and envelope-stress conditions?
Experiment: Construct single and combinatorial ddl depletion strains and test D-Ala-D-Ala auxotrophy, muropeptide composition, and envelope integrity.
Type: conditional genetics and peptidoglycan phenotyping
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