DdlB is a cytoplasmic D-alanine-D-alanine ligase of Pseudomonas putida KT2440 and one of three annotated Ddl-family paralogs. It uses ATP and magnesium or manganese to form the D-Ala-D-Ala dipeptide incorporated by MurF into the peptidoglycan stem pentapeptide.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Correct ATP-binding property ancillary to dipeptide ligation. Reason: DdlB consumes ATP, but D-alanine-D-alanine ligase activity is its core function. Supporting Evidence: file:PSEPK/ddlB/ddlB-uniprot.txt Reaction=2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate + |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Correct localization for soluble D-Ala-D-Ala synthesis. Reason: UniProt explicitly assigns Q88N74 to the cytoplasm. Supporting Evidence: file:PSEPK/ddlB/ddlB-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005829 cytosol | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Biologically compatible but redundant with the cytoplasm annotation. Reason: For this bacterial soluble enzyme the separate cytosol term adds no useful information beyond the cytoplasm assignment and is omitted from the core-function summary. |
| GO:0008716 D-alanine-D-alanine ligase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Correct and specific core molecular function. Reason: UniProt assigns EC 6.3.2.4 and direct formation of D-Ala-D-Ala. Supporting Evidence: file:PSEPK/ddlB/ddlB-uniprot.txt Reaction=2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate + |
| GO:0009252 peptidoglycan biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Correct core biological process. Reason: UniProt places Q88N74 in peptidoglycan biosynthesis. Supporting Evidence: file:PSEPK/ddlB/ddlB-uniprot.txt PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Correct but broad ancillary cofactor-binding property. Reason: DdlB binds magnesium or manganese for catalysis, while the exact ligase activity remains the informative core function. Supporting Evidence: file:PSEPK/ddlB/ddlB-uniprot.txt Note=Binds 2 magnesium or manganese ions per subunit. |
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Download this section (compressed HTML)Q: What is the intrinsic susceptibility of KT2440 DdlB to D-cycloserine?
Experiment: Measure purified Q88N74 inhibition by D-cycloserine and compare with cellular susceptibility and ddlB-resistant mutants.
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Download this section (compressed HTML)Q88N74/PP_1339 forms D-Ala-D-Ala for peptidoglycan stem-peptide assembly
[UniProtKB:Q88N74, "Reaction=2 D-alanine + ATP = D-alanyl-D-alanine + ADP +
phosphate +"; "PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis."].
ATP and metal binding are ancillary. Cytoplasm is retained as the supported
location, while the duplicate cytosol term is marked over-annotated and omitted
from the core function.
For the focused precursor-supply module, Q88N74 is one of two KT2440 proteins
assigned to the DdlB-like PTHR23132:SF23 branch. It and PP_5673 are represented
as exemplars of one family variant because current evidence does not establish
different reactions or deployment conditions. DdlA/Q88EV6 belongs to the
separate SF25 branch.
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