LigA is the essential NAD-dependent DNA ligase of Escherichia coli. It seals adjacent 3′ hydroxyl and 5′ phosphate DNA ends through an enzyme-adenylate intermediate, using NAD+ as the adenylate donor. LigA joins nicks after Okazaki-fragment maturation and during DNA repair, acting in the cytoplasm on chromosomal DNA. Its BRCT domain assists DNA binding but is not indispensable for nick sealing.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IDA PMID:15848142 Analysis of ligation and DNA binding by Escherichia coli DNA... | ACCEPT | Summary: Purified LigA and its BRCT domain bind DNA; binding contributes to substrate recognition without a demonstrated sequence-specific preference.. Reason: Purified LigA and its BRCT domain bind DNA; binding contributes to substrate recognition without a demonstrated sequence-specific preference. Supporting Evidence: |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: Purified LigA and its BRCT domain bind DNA; binding contributes to substrate recognition without a demonstrated sequence-specific preference.. Reason: Purified LigA and its BRCT domain bind DNA; binding contributes to substrate recognition without a demonstrated sequence-specific preference. Supporting Evidence: |
| GO:0003911 DNA ligase (NAD+) activity | IBA GO_REF:0000033 | ACCEPT | Summary: LigA catalyzes NAD-dependent DNA nick joining. Reason: LigA catalyzes NAD-dependent DNA nick joining. Modern purified-enzyme and mutational evidence corroborates the historical ligation annotations even where an early article has no cached abstract. PAINT lineage-loss inspection found no applicable IRD/IKR; the IBA is evaluated as an ancestral-function judgment, not by counting listed donors. Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
| GO:0003911 DNA ligase (NAD+) activity | IDA PMID:15583169 Characterization of a temperature-sensitive DNA ligase from ... | ACCEPT | Summary: LigA catalyzes NAD-dependent DNA nick joining. Reason: LigA catalyzes NAD-dependent DNA nick joining. Modern purified-enzyme and mutational evidence corroborates the historical ligation annotations even where an early article has no cached abstract. Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
| GO:0003911 DNA ligase (NAD+) activity | IDA PMID:4291949 Enzymatic joining of DNA strands: a novel reaction of diphos... | ACCEPT | Summary: LigA catalyzes NAD-dependent DNA nick joining. Reason: LigA catalyzes NAD-dependent DNA nick joining. Modern purified-enzyme and mutational evidence corroborates the historical ligation annotations even where an early article has no cached abstract. Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
| GO:0003911 DNA ligase (NAD+) activity | IDA PMID:4295585 Enzymatic joining of DNA strands, II. An enzyme-adenylate in... | ACCEPT | Summary: LigA catalyzes NAD-dependent DNA nick joining. Reason: LigA catalyzes NAD-dependent DNA nick joining. Modern purified-enzyme and mutational evidence corroborates the historical ligation annotations even where an early article has no cached abstract. Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
| GO:0003911 DNA ligase (NAD+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: LigA catalyzes NAD-dependent DNA nick joining. Reason: LigA catalyzes NAD-dependent DNA nick joining. Modern purified-enzyme and mutational evidence corroborates the historical ligation annotations even where an early article has no cached abstract. Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
| GO:0005515 protein binding | IPI PMID:15690043 Interaction network containing conserved and essential prote... | REMOVE | Summary: The reported interaction does not specify a useful molecular function. Reason: This row reports binding of ligA to UniProtKB:P07813 from PMID:15690043. Bare protein binding is uninformative under the project policy; removing the annotation does not deny the interaction. A partner list alone does not justify transferring the partner’s catalytic activity. Source availability and the distinction between focused interaction assays and large-scale screens are recorded in the reference notes. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric... | REMOVE | Summary: The reported interaction does not specify a useful molecular function. Reason: This row reports binding of ligA to UniProtKB:P07813 from PMID:24561554. Bare protein binding is uninformative under the project policy; removing the annotation does not deny the interaction. A partner list alone does not justify transferring the partner’s catalytic activity. Source availability and the distinction between focused interaction assays and large-scale screens are recorded in the reference notes. Supporting Evidence: |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: The soluble chromosome-replication machinery acts in the bacterial cytosol. Reason: The soluble chromosome-replication machinery acts in the bacterial cytosol. The experimental localization annotation is consistent with the established protein architecture; a proteomics citation is not treated as a new single-protein microscopy experiment. PAINT lineage-loss inspection found no applicable IRD/IKR; the IBA is evaluated as an ancestral-function judgment, not by counting listed donors. |
| GO:0005829 cytosol | IDA PMID:15911532 Localization, annotation, and comparison of the Escherichia ... | ACCEPT | Summary: The soluble chromosome-replication machinery acts in the bacterial cytosol. Reason: The soluble chromosome-replication machinery acts in the bacterial cytosol. The experimental localization annotation is consistent with the established protein architecture; a proteomics citation is not treated as a new single-protein microscopy experiment. Supporting Evidence: |
| GO:0005829 cytosol | IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol. | ACCEPT | Summary: The soluble chromosome-replication machinery acts in the bacterial cytosol. Reason: The soluble chromosome-replication machinery acts in the bacterial cytosol. The experimental localization annotation is consistent with the established protein architecture; a proteomics citation is not treated as a new single-protein microscopy experiment. Supporting Evidence: |
| GO:0005829 cytosol | IDA PMID:23630273 Single-molecule DNA repair in live bacteria. | ACCEPT | Summary: The soluble chromosome-replication machinery acts in the bacterial cytosol. Reason: The soluble chromosome-replication machinery acts in the bacterial cytosol. The experimental localization annotation is consistent with the established protein architecture; a proteomics citation is not treated as a new single-protein microscopy experiment. Supporting Evidence: |
| GO:0006259 DNA metabolic process | IEA GO_REF:0000104 | MODIFY | Summary: LigA directly seals DNA nicks during replication and repair. Reason: LigA directly seals DNA nicks during replication and repair. These two supported processes refine the broad DNA-metabolism annotation without dropping either role. Proposed replacements: DNA replication DNA repair Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
| GO:0006260 DNA replication | IEA GO_REF:0000002 | ACCEPT | Summary: ligA directly participates in the chromosome-replication machinery through the activity described in its core function. Reason: ligA directly performs NAD-dependent DNA nick sealing within the replication machinery. This supports participation in chromosome replication; the pathway-level term remains informative alongside the specific molecular function and subcomplex assignments. Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | ACCEPT | Summary: Live-cell single-molecule observations follow LigA nick-sealing reactions and increased activity after DNA methylation damage. Reason: Live-cell single-molecule observations follow LigA nick-sealing reactions and increased activity after DNA methylation damage. Repair is a direct catalytic role rather than only a mutant-survival phenotype. Supporting Evidence: |
| GO:0070403 NAD+ binding | IMP PMID:11781321 Conserved residues in domain Ia are required for the reactio... | ACCEPT | Summary: NAD+ is the adenylate donor for LigA. Reason: NAD+ is the adenylate donor for LigA. Its binding is chemically distinct from NAD-dependent oxidoreductase chemistry and supports the experimentally characterized ligation mechanism. Supporting Evidence: PMID:15848142 NAD(+)-dependent DNA ligases are essential enzymes in bacteria, with the most widely studied of this class of enzymes being LigA from Escherichia coli. |
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