LIG3 encodes DNA ligase III, an ATP-dependent DNA ligase (EC 6.5.1.1) that seals single-strand nicks in duplex DNA through an enzyme-AMP intermediate. It has an N-terminal PARP-type zinc finger that, with the DNA-binding domain, senses nicks and DNA ends and hands them to the nucleotidyltransferase/OB-fold catalytic core. Alternative translation initiation gives two forms: isoform 1, with an N-terminal mitochondrial transit peptide, is imported into mitochondria, where LIG3 is the only DNA ligase and seals Okazaki fragments during mtDNA replication and nicks in mitochondrial base excision repair; isoform 3 (LIG3alpha) is nuclear and forms a stable BRCT-mediated heterodimer with XRCC1, which imports and stabilizes it. Nuclear LIG3alpha/XRCC1 ligates nicks in short-patch base excision and single-strand break repair, can complete nucleotide excision repair (alongside LIG1), and is the main ligase of the microhomology-biased alternative end-joining pathway of double-strand break repair, being recruited to such breaks by MRN. A germ-cell splice form (LIG3beta) lacks the BRCT domain. The mitochondrial function is the essential one: nuclear LIG3 is dispensable in mouse cells, where LIG1 can substitute, whereas loss of mitochondrial LIG3 depletes mtDNA, and biallelic human LIG3 variants cause a mitochondrial neurogastrointestinal encephalomyopathy-like mtDNA depletion syndrome. LIG3 does not take part in V(D)J recombination.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000724 double-strand break repair via homologous recombination | TAS Reactome:R-HSA-5693538 | MODIFY | Summary: Reactome places LIG3 in its Homology Directed Repair pathway, which in Reactome groups homologous recombination, single strand annealing and microhomology-mediated end joining (MMEJ). LIG3 participates only in the MMEJ branch. Reason: LIG3 has no demonstrated role in homologous recombination; its inclusion in the Reactome HDR pathway derives from the MMEJ sub-pathway, where LIG3:XRCC1 seals the remaining nicks. MMEJ is alternative NHEJ, not HR, so the annotation should be moved to GO:0097681 (already carried by the gene via ARBA, and supported experimentally). Proposed replacements: double-strand break repair via alternative nonhomologous end joining Supporting Evidence: Reactome:R-HSA-5693538 HDR preferably occurs through the error-free homologous recombination repair (HRR), but can also occur through the error-prone single strand annealing (SSA), or the least accurate microhomology-mediated end j Reactome:R-HSA-5687675 LIG3:XRCC1 is recruited to MMEJ sites by the MRN complex and ligates single strand nicks that remain after reparative DNA synthesis PMID:21816818 MRN interacts with DNA ligase IIIΞ±/XRCC1, stimulating intermolecular ligation, and together these proteins join incompatible DNA ends in a reaction that mimics alt-NHEJ. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-based DNA binding. LIG3 binds DNA through its PARP-like zinc finger, DNA-binding domain and catalytic core; DNA binding is an intrinsic part of nick sensing and ligation. Reason: Correct (structural and mutational data show ZnF and DBD nick/end binding), but DNA binding here is a component of the ligase mechanism rather than a separate function. No more specific DNA-binding term is clearly better supported than the ligase activity itself, so keep as non-core. Supporting Evidence: PMID:20518483 the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis |
| GO:0003909 DNA ligase activity | IDA PMID:19589734 Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta,... | MODIFY | Summary: DNA ligase activity of purified LIG3 (LigIIIalpha/XRCC1 and LigIIIbeta) on nicked and linear duplex DNA substrates. Reason: LIG3 is an ATP-dependent DNA ligase (EC 6.5.1.1) that forms an enzyme-adenylate intermediate; the more specific child GO:0003910 DNA ligase (ATP) activity, which the gene already carries by EXP and IBA, is the correct term. Proposed replacements: DNA ligase (ATP) activity Supporting Evidence: PMID:19589734 hLigIIIbeta and the hLigIIIalpha/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates PMID:19589734 In eukaryotes, DNA ligases react with ATP to form a covalent enzyme-adenylate intermediate. |
| GO:0003909 DNA ligase activity | IDA PMID:9809069 DNA ligase IV is essential for V(D)J recombination and DNA d... | MODIFY | Summary: Grawunder et al. 1998 complemented LIG4-null pre-B cells with DNA ligases I, III and IV; LIG3 was expressed but could not substitute for LIG4 in NHEJ. The annotation of LIG3 ligase activity from this paper rests on full text not in the cache (abstract only). Reason: The abstract does not report LIG3 ligase activity directly, but LIG3 ligase activity is not in doubt (PMID:19589734, PMID:20518483) and the UniProt curator made this annotation from the full text. As for the other GO:0003909 rows, the specific ATP-dependent child term is preferable. Proposed replacements: DNA ligase (ATP) activity Supporting Evidence: PMID:9809069 This phenotype can only be reversed by complementation with DNA ligase IV but not by expression of either of the remaining two ligases, DNA ligase I or III. PMID:19589734 hLigIIIbeta and the hLigIIIalpha/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates |
| GO:0003909 DNA ligase activity | IEA GO_REF:0000120 | MODIFY | Summary: Electronic DNA ligase activity from orthologs and the InterPro DNA ligase signature. Reason: Correct but less specific than GO:0003910 DNA ligase (ATP) activity, which LIG3 carries experimentally and by IBA; LIG3 is an ATP-dependent ligase. Proposed replacements: DNA ligase (ATP) activity Supporting Evidence: file:human/LIG3/LIG3-uniprot.txt Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate.; EC=6.5.1.1 |
| GO:0003909 DNA ligase activity | TAS Reactome:R-HSA-5649734 | MODIFY | Summary: Reactome reaction in which LIG3 ligates the NEIL1/NEIL2-generated single-strand break after POLB gap filling in BER. Reason: The reaction is ATP-dependent nick sealing; use the specific child GO:0003910. Proposed replacements: DNA ligase (ATP) activity Supporting Evidence: Reactome:R-HSA-5649734 LIG3 (DNA ligase 3) ligates the two DNA strand fragments at the single strand break (SSB), thus completing the base excision repair |
| GO:0003909 DNA ligase activity | TAS Reactome:R-HSA-5687675 | MODIFY | Summary: Reactome reaction in which LIG3:XRCC1 ligates remaining single-strand nicks in MMEJ. Reason: The reaction is ATP-dependent nick sealing; use the specific child GO:0003910. Proposed replacements: DNA ligase (ATP) activity Supporting Evidence: Reactome:R-HSA-5687675 LIG3:XRCC1 is recruited to MMEJ sites by the MRN complex and ligates single strand nicks that remain after reparative DNA synthesis |
| GO:0003909 DNA ligase activity | TAS Reactome:R-HSA-73931 | MODIFY | Summary: Reactome reaction in which LIG3, recruited by XRCC1, ligates the repaired strand in single-nucleotide BER. Reason: The reaction is ATP-dependent nick sealing; use the specific child GO:0003910. Proposed replacements: DNA ligase (ATP) activity Supporting Evidence: Reactome:R-HSA-73931 ligates the two DNA strand fragments, thus completing the base excision repair |
| GO:0003910 DNA ligase (ATP) activity | EXP PMID:10207110 The human DNA ligase III gene encodes nuclear and mitochondr... | ACCEPT | Summary: Lakshmipathy and Campbell showed DNA ligase activity in mitochondrial extracts depends on LIG3 (antisense depletion reduced mitochondrial ligase activity). Reason: ATP-dependent DNA ligase activity is the core catalytic function of LIG3 in both nucleus and mitochondria; UniProt cites this paper for the EC 6.5.1.1 reaction. Supporting Evidence: PMID:10207110 mitochondrial protein extracts prepared from human cells overexpressing antisense DNA ligase III mRNA possessed substantially less DNA ligase activity than did mitochondrial extracts prepared from control cells |
| GO:0003910 DNA ligase (ATP) activity | EXP PMID:20518483 Human DNA ligase III recognizes DNA ends by dynamic switchin... | ACCEPT | Summary: Structural and biochemical study of LIG3 showing ZnF-dependent nick sensing and nick joining by the catalytic core. Reason: Direct biochemical evidence of LIG3 nick ligation, with crystal structure of the catalytic region bound to nicked DNA. Supporting Evidence: PMID:20518483 The collective results support a "jackknife model" in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. file:human/LIG3/LIG3-uniprot.txt The PARP-type zinc finger is required for DNA ligase activity. |
| GO:0003910 DNA ligase (ATP) activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for ATP-dependent DNA ligase activity, from a node ancestral to LIG1 and LIG3, with LIG3 itself among the experimental sources. Reason: ATP-dependent ligase activity is ancestral in the LIG1/LIG3 lineage and is experimentally confirmed for LIG3. Supporting Evidence: PMID:19589734 hLigIIIbeta and the hLigIIIalpha/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates |
| GO:0003910 DNA ligase (ATP) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic EC 6.5.1.1 / InterPro mapping to DNA ligase (ATP) activity. Reason: Matches the experimentally established activity. Supporting Evidence: file:human/LIG3/LIG3-uniprot.txt Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate.; EC=6.5.1.1 |
| GO:0005515 protein binding | IPI PMID:15744309 Defective DNA single-strand break repair in spinocerebellar ... | REMOVE | Summary: Interaction with TDP1, which is sequestered into SSBR complexes through direct interaction with DNA ligase IIIalpha. Reason: Bare protein binding is uninformative. The LIG3-TDP1 interaction is real and places LIG3 in SSBR complexes (captured by single strand break repair), but the interaction itself is not evidence of a more specific molecular function of LIG3. Supporting Evidence: PMID:15744309 We report that TDP1 is sequestered into multi-protein single-strand break repair (SSBR) complexes by direct interaction with DNA ligase IIIalpha |
| GO:0005515 protein binding | IPI PMID:19336415 Human DNA polymerase beta polymorphism, Arg137Gln, impairs i... | REMOVE | Summary: Interaction with POLB from a study of the POLB R137Q polymorphism. Reason: Bare protein binding is uninformative; the POLB-LIG3 association reflects their shared BER complex, which is captured by the base-excision repair process term. |
| GO:0005515 protein binding | IPI PMID:19589734 Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta,... | REMOVE | Summary: Interaction with XRCC1 (LigIIIalpha/XRCC1 complex purified for kinetics). Reason: Bare protein binding is uninformative. The stable XRCC1 heterodimer is captured by the cellular component GO:0070421 DNA ligase III-XRCC1 complex, which is accepted in this review. Supporting Evidence: PMID:33087283 The XRCC1 C-terminal BRCT2 domain forms a strong complex with LIG3 [9] that is required for LIG3 nuclear localization [10]. |
| GO:0005515 protein binding | IPI PMID:24407287 Promyelocytic leukemia protein interacts with the apoptosis-... | REMOVE | Summary: Interaction with PYCARD (ASC) reported in a study of PML and inflammasome activation; abstract only. Reason: Bare protein binding is uninformative and there is no functional context linking LIG3 to inflammasome biology. |
| GO:0005515 protein binding | IPI PMID:25609649 Proteomic analyses reveal distinct chromatin-associated and ... | REMOVE | Summary: Interaction with MAX from a proteomic survey of transcription factor complexes. Reason: Bare protein binding from a high-throughput survey; uninformative and without functional follow-up for LIG3. |
| GO:0005515 protein binding | IPI PMID:33855352 Biallelic variants in LIG3 cause a novel mitochondrial neuro... | REMOVE | Summary: Interaction with POLG reported in the LIG3 MNGIE-like disease paper. Reason: Bare protein binding is uninformative. The LIG3-POLG association is relevant to mtDNA replication, which is captured by the mitochondrial DNA replication process term proposed in this review. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based ATP binding; ATP is the adenylate donor for the ligase reaction. Reason: LIG3 is an ATP-dependent ligase that forms a lysyl-AMP intermediate (active site K508); ATP binding is required for catalysis. Supporting Evidence: PMID:19589734 In eukaryotes, DNA ligases react with ATP to form a covalent enzyme-adenylate intermediate. |
| GO:0005634 nucleus | EXP PMID:10207110 The human DNA ligase III gene encodes nuclear and mitochondr... | ACCEPT | Summary: Nuclear localization of the downstream-initiated LIG3 isoform (isoform 3, alpha). Reason: The nuclear form lacks the transit peptide and accumulates in the nucleus, where it partners XRCC1 in BER/SSBR and alternative NHEJ. Supporting Evidence: PMID:10207110 inactivation of the upstream ATG resulted in nuclear accumulation of the DNA ligase III protein |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for nucleus across DNA ligases I/III/IV and fungal/plant orthologs. Reason: Consistent with experimental localization of LIG3 isoform 3 in the nucleus. Supporting Evidence: PMID:10207110 inactivation of the upstream ATG resulted in nuclear accumulation of the DNA ligase III protein |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to nucleus (isoforms 3 and 4). Reason: Consistent with experimental nuclear localization of the alpha isoform. Supporting Evidence: PMID:10207110 inactivation of the upstream ATG resulted in nuclear accumulation of the DNA ligase III protein |
| GO:0005634 nucleus | NAS PMID:33087283 XRCC1 - Strategies for coordinating and assembling a versati... | ACCEPT | Summary: ComplexPortal NAS for nucleus based on a review of XRCC1 that describes XRCC1-dependent nuclear import of LIG3. Reason: Consistent with experimental nuclear localization; XRCC1 binding is required for LIG3 nuclear localization. Supporting Evidence: PMID:33087283 The XRCC1 C-terminal BRCT2 domain forms a strong complex with LIG3 [9] that is required for LIG3 nuclear localization [10]. |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: Nucleoplasm, from HPA immunofluorescence. Reason: The nuclear LIG3 isoform acts on chromosomal DNA in the nucleoplasm (BER/SSBR, alt-NHEJ, NER ligation). Supporting Evidence: Reactome:R-HSA-73931 ligates the two DNA strand fragments, thus completing the base excision repair |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-110376 | ACCEPT | Summary: Reactome nucleoplasm location for recruitment of LIG3:XRCC1 by POLB in BER. Reason: Nuclear BER reactions occur in the nucleoplasm; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-110376 POLB recruits XRCC1:LIG3 complex, consisting of DNA repair protein XRCC1 and DNA ligase 3, to the DNA containing a single nucleotide gap |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-110380 | ACCEPT | Summary: Reactome nucleoplasm location for dissociation of LIG3:XRCC1 from the BER site. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-110380 After the base excision repair is completed, the complex of XRCC1 with LIG3 (DNA ligase 3), and POLB (DNA polymerase beta) dissociate from the repaired DNA |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5649705 | ACCEPT | Summary: Reactome nucleoplasm location for PNKP action in NEIL1/NEIL2 BER, with LIG3:XRCC1 in the complex. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5649726 LIG3:XRCC1, a complex of DNA ligase 3 and DNA repair protein XRCC1, is recruited to the single nucleotide gap at the SSB (single strand break) site bound by NEIL1 or NEIL2 |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5649723 | ACCEPT | Summary: Reactome nucleoplasm location for POLB gap filling in NEIL1/NEIL2 BER. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5649726 LIG3:XRCC1, a complex of DNA ligase 3 and DNA repair protein XRCC1, is recruited to the single nucleotide gap at the SSB (single strand break) site bound by NEIL1 or NEIL2 |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5649724 | ACCEPT | Summary: Reactome nucleoplasm location for dissociation of LIG3:XRCC1, POLB, NEIL1/2 and PNKP after BER. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5649724 NEIL1 or NEIL2, POLB, LIG3:XRCC1 and PNKP dissociate from repaired DNA |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5649726 | ACCEPT | Summary: Reactome nucleoplasm location for recruitment of LIG3:XRCC1 and PNKP to the NEIL-generated SSB. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5649726 LIG3:XRCC1, a complex of DNA ligase 3 and DNA repair protein XRCC1, is recruited to the single nucleotide gap at the SSB (single strand break) site bound by NEIL1 or NEIL2 |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5649734 | ACCEPT | Summary: Reactome nucleoplasm location for LIG3 ligation of the NEIL-generated SSB. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5649734 LIG3 (DNA ligase 3) ligates the two DNA strand fragments at the single strand break (SSB), thus completing the base excision repair |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5687673 | ACCEPT | Summary: Reactome nucleoplasm location for MRN recruitment of LIG3:XRCC1 to MMEJ sites. Reason: Nuclear alt-NHEJ context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5687673 The MRN complex recruits DNA ligase 3 (LIG3) bound to XRCC1 (LIG3:XRCC1) to microhomology-mediated end joining (MMEJ) sites |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5687675 | ACCEPT | Summary: Reactome nucleoplasm location for LIG3 ligation of remaining nicks in MMEJ. Reason: Nuclear alt-NHEJ context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5687675 LIG3:XRCC1 is recruited to MMEJ sites by the MRN complex and ligates single strand nicks that remain after reparative DNA synthesis |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-5690997 | ACCEPT | Summary: Reactome nucleoplasm location for repair-patch ligation in GG-NER (LIG1 or LIG3). Reason: Nuclear NER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-5690997 Two DNA ligases, LIG1 and LIG3, can perform the ligation in global genome NER (GG-NER) |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782227 | ACCEPT | Summary: Reactome nucleoplasm location for repair-patch ligation in TC-NER (LIG1 or LIG3). Reason: Nuclear NER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-6782227 Two DNA ligases, LIG1 and LIG3, can perform the ligation in transcription-coupled NER (TC-NER) |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-73931 | ACCEPT | Summary: Reactome nucleoplasm location for LIG3 ligation in single-nucleotide BER. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-73931 ligates the two DNA strand fragments, thus completing the base excision repair |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-73932 | ACCEPT | Summary: Reactome nucleoplasm location for POLB resynthesis in single-nucleotide BER, where LIG3:XRCC1 is part of the complex. Reason: Nucleoplasmic BER context; consistent with nuclear isoform localization. Supporting Evidence: Reactome:R-HSA-110376 POLB recruits XRCC1:LIG3 complex, consisting of DNA repair protein XRCC1 and DNA ligase 3, to the DNA containing a single nucleotide gap |
| GO:0005739 mitochondrion | EXP PMID:10207110 The human DNA ligase III gene encodes nuclear and mitochondr... | ACCEPT | Summary: Mitochondrial localization of the upstream-initiated isoform (isoform 1), shown with GFP fusions and epitope-tagged minigenes, and by LIG3-dependent mitochondrial ligase activity. Reason: Direct evidence (root organelle term, assay does not resolve sub-compartment). Mitochondrial LIG3 is the essential form of the gene. Supporting Evidence: PMID:10207110 inactivation of the downstream ATG abolished nuclear localization and led to accumulation within the mitochondrial compartment PMID:21390132 we find that the mitochondrial, but not nuclear, Lig3 is required for cellular viability |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: Detection in a high-confidence human mitochondrial proteome. Reason: Organelle proteomics agrees with targeted localization studies; root organelle term is appropriate for this assay. Supporting Evidence: PMID:10207110 inactivation of the downstream ATG abolished nuclear localization and led to accumulation within the mitochondrial compartment |
| GO:0005739 mitochondrion | IDA PMID:24674627 Overexpression of DNA ligase III in mitochondria protects ce... | ACCEPT | Summary: Mitochondrially targeted LIG3 in purified mitochondrial extracts improves mitochondrial BER. Reason: Direct functional evidence that LIG3 acts in mitochondria. Supporting Evidence: PMID:24674627 Overexpression of DNA ligase III in mitochondria improved the rate of overall BER |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping to mitochondrion (isoforms 1 and 2). Reason: Rests on the curated, experimentally supported isoform 1 mitochondrial location and transit peptide (UniProt TRANSIT 1..42). Supporting Evidence: file:human/LIG3/LIG3-uniprot.txt Isoform 1 is targeted to mitochondria, where it functions as a DNA ligase in mitochondrial base-excision DNA repair |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9914903 | ACCEPT | Summary: Reactome places mitochondrial LIG3 (isoform 1) in the matrix, ligating nascent mtDNA strands. Reason: mtDNA, its replication and repair are in the matrix (nucleoids); the transit peptide-directed import and the function on mtDNA together support the matrix sub-compartment. Supporting Evidence: Reactome:R-HSA-9914903 the resulting single-stranded gaps are ligated by the mitochondrial isoform of ligase III (LIG3 isoform 1) PMID:21878356 These findings support the role of DNA ligase III as the replicative DNA ligase in human mtDNA replication |
| GO:0006273 lagging strand elongation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA for lagging strand elongation from the node ancestral to LIG1 and LIG3, seeded by yeast CDC9 and fission yeast Cdc17. Reason: LIG3 is the Okazaki-fragment ligase in mitochondrial DNA replication; in the nucleus LIG1 is the replicative ligase and LIG3 only backs it up. Lagging strand elongation is therefore true of LIG3 mainly in the mitochondrial context, which is better captured by mitochondrial DNA replication. Supporting Evidence: PMID:21878356 we propose that DNA ligase III is responsible for the ligation of Okazaki fragments in human mitochondria |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based DNA repair. Reason: Broad but correct; LIG3 participates in several DNA repair pathways (BER, SSBR, alt-NHEJ, mtDNA repair, NER ligation). More specific terms are also annotated. Supporting Evidence: PMID:33087283 The XRCC1 scaffold has been found to support two related DNA repair pathways: base excision repair (BER) and single-strand break repair (SSBR), while LIG3 participates in these and other pathways including nucleotide excision repair [3] and alternate non-homologous end joining (alt-NHEJ) [4]. |
| GO:0006282 regulation of DNA repair | NAS PMID:33087283 XRCC1 - Strategies for coordinating and assembling a versati... | MARK AS OVER ANNOTATED | Summary: ComplexPortal NAS for regulation of DNA repair, based on an XRCC1 review. Reason: LIG3 executes the ligation step of DNA repair; the review discusses XRCC1 controlling LIG3 involvement, not LIG3 regulating repair. The participation is captured by the DNA repair process terms; a regulatory role for LIG3 is not supported. Supporting Evidence: PMID:33087283 The tether to XRCC1 may help to control the involvement of LIG3 in different repair processes. |
| GO:0006284 base-excision repair | IDA PMID:19589734 Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta,... | ACCEPT | Summary: Base-excision repair; the cited paper characterizes LigIIIalpha/XRCC1 ligation of nicked substrates mimicking repair intermediates. Reason: LIG3 (with XRCC1) seals the nick in short-patch BER (Reactome; XRCC1 literature), and mitochondrial LIG3 performs mtBER. In mouse cells LIG1 can substitute in nuclear repair, but LIG3 participation in BER is well established. Supporting Evidence: PMID:19589734 Here we have quantitated and compared the activities of purified recombinant hLigI, hLigIIIΞ±/XRCC1, hLigIIIΞ² and hLigIV/XRCC4 on DNA substrates that mimic DNA nicks and double strand breaks that are repaired in vivo. Reactome:R-HSA-73931 ligates the two DNA strand fragments, thus completing the base excision repair |
| GO:0006287 base-excision repair, gap-filling | TAS Reactome:R-HSA-110381 | MODIFY | Summary: Reactome pathway "Resolution of AP sites via the single-nucleotide replacement pathway" mapped to base-excision repair, gap-filling. Reason: Gap filling is done by POLB; LIG3 performs the subsequent nick ligation in short-patch BER. Its participation is in base-excision repair (GO:0006284), already accepted for this gene. Proposed replacements: base-excision repair Supporting Evidence: Reactome:R-HSA-73931 ligates the two DNA strand fragments, thus completing the base excision repair |
| GO:0006287 base-excision repair, gap-filling | TAS Reactome:R-HSA-5649702 | MODIFY | Summary: Reactome pathway "APEX1-independent resolution of AP sites via the single nucleotide replacement pathway" mapped to base-excision repair, gap-filling. Reason: Gap filling is done by POLB; LIG3 performs the nick ligation in NEIL1/NEIL2-initiated BER. Its participation is in base-excision repair (GO:0006284). Proposed replacements: base-excision repair Supporting Evidence: Reactome:R-HSA-5649734 LIG3 (DNA ligase 3) ligates the two DNA strand fragments at the single strand break (SSB), thus completing the base excision repair |
| GO:0006302 double-strand break repair | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for double-strand break repair from the LIG3 clade node, seeded by LIG3 and mouse and zebrafish orthologs. Reason: LIG3/XRCC1 is a ligase of the alternative (microhomology-mediated) end-joining pathway of DSB repair; supported by biochemical, mouse cell and human extract evidence. Supporting Evidence: PMID:15899791 These in vivo and in vitro observations identify DNA ligase III as a candidate component for B-NHEJ PMID:21655080 two alt-NHEJ pathways, one that is biased toward microhomology use and requires Lig3 |
| GO:0006302 double-strand break repair | IDA PMID:19589734 Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta,... | ACCEPT | Summary: LigIIIalpha/XRCC1 shows robust intermolecular ligation of linear duplex DNA, consistent with a role in alternative NHEJ of DSBs. Reason: Consistent with LIG3's established role in alt-NHEJ DSB repair. Supporting Evidence: PMID:19589734 Thus, the robust intermolecular ligation activity of hLigIIIΞ±/XRCC1 is consistent with the participation of this complex in alternative NHEJ. |
| GO:0006310 DNA recombination | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro-based DNA recombination. Reason: The mapping comes from the generic ATP-dependent ligase domains. LIG3 has no demonstrated role in homologous recombination or V(D)J recombination (the latter is explicitly negated); its contribution to chromosomal translocations is via alt-NHEJ repair, better captured by GO:0097681. Supporting Evidence: PMID:9809069 This phenotype can only be reversed by complementation with DNA ligase IV but not by expression of either of the remaining two ligases, DNA ligase I or III. |
| GO:0007005 mitochondrion organization | IEA GO_REF:0000117 | MODIFY | Summary: ARBA prediction of mitochondrion organization. Reason: LIG3 does not organize mitochondria; it maintains mtDNA by ligating Okazaki fragments and repair intermediates. Loss of Lig3 causes mtDNA depletion and secondary mitochondrial dysfunction. The appropriate term is mitochondrial DNA metabolic process (GO:0000002 mitochondrial genome maintenance is obsolete), with replication and repair children captured elsewhere. Proposed replacements: mitochondrial DNA metabolic process Supporting Evidence: PMID:21390131 Inactivation of Lig3 in the mouse nervous system resulted in mtDNA loss leading to profound mitochondrial dysfunction PMID:33855352 We demonstrated that the LIG3 gene defects affect mtDNA maintenance, leading to mtDNA depletion without the accumulation of multiple deletions |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based zinc ion binding via the PARP-type zinc finger. Reason: The N-terminal PARP-type ZnF (Cys ligands at 105, 108, 139, 142 in UniProt) binds zinc and is required for DNA nick sensing and ligase activity. Supporting Evidence: file:human/LIG3/LIG3-uniprot.txt The PARP-type zinc finger is required for DNA ligase activity. |
| GO:0031981 nuclear lumen | IEA GO_REF:0000117 | MODIFY | Summary: ARBA prediction of nuclear lumen. Reason: Correct but general; the gene already carries nucleoplasm (HPA IDA, Reactome), the more specific part of the nuclear lumen where LIG3 acts. Proposed replacements: nucleoplasm Supporting Evidence: PMID:10207110 inactivation of the upstream ATG resulted in nuclear accumulation of the DNA ligase III protein |
| GO:0033151 V(D)J recombination | IDA NOT PMID:9809069 DNA ligase IV is essential for V(D)J recombination and DNA d... | ACCEPT | Summary: NOT V(D)J recombination. LIG3 expression did not rescue V(D)J recombination in LIG4-null human pre-B cells. Reason: The negation is directly supported; only LIG4 restored V(D)J recombination. Supporting Evidence: PMID:9809069 This phenotype can only be reversed by complementation with DNA ligase IV but not by expression of either of the remaining two ligases, DNA ligase I or III. |
| GO:0043504 mitochondrial DNA repair | IDA PMID:24674627 Overexpression of DNA ligase III in mitochondria protects ce... | ACCEPT | Summary: Mitochondrial LIG3 overexpression increases the rate of mitochondrial BER and survival after oxidative stress. Reason: LIG3 isoform 1 is the only mtDNA ligase and seals mtBER intermediates; core function. Supporting Evidence: PMID:24674627 Overexpression of DNA ligase III in mitochondria improved the rate of overall BER, increased cell survival after menadione induced oxidative stress PMID:33855352 The LIG3 gene encodes the only mitochondrial DNA (mtDNA) ligase and therefore plays a pivotal role in mtDNA repair and replication. |
| GO:0043504 mitochondrial DNA repair | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of mitochondrial DNA repair. Reason: Matches experimental evidence for the mitochondrial isoform. Supporting Evidence: PMID:24674627 Overexpression of DNA ligase III in mitochondria improved the rate of overall BER |
| GO:0051053 negative regulation of DNA metabolic process | IEA GO_REF:0000117 | REMOVE | Summary: ARBA prediction of negative regulation of DNA metabolic process. Reason: No evidence that LIG3 negatively regulates DNA metabolism; it is a catalytic participant in DNA replication and repair. The rule likely echoes the mis-signed IMP annotation of negative regulation of mtDNA replication, whose source paper shows the opposite (LIG3 knockdown impairs mtDNA replication). Supporting Evidence: PMID:21878356 DNA ligase III knockdown attenuated the recovery of mtDNA copy number |
| GO:0070421 DNA ligase III-XRCC1 complex | NAS PMID:33087283 XRCC1 - Strategies for coordinating and assembling a versati... | ACCEPT | Summary: ComplexPortal NAS for the DNA ligase III-XRCC1 complex. Reason: The LIG3alpha-XRCC1 heterodimer (BRCT-BRCT interaction) is well established; it stabilizes LIG3 and imports it into the nucleus. Supporting Evidence: PMID:33087283 The XRCC1 C-terminal BRCT2 domain forms a strong complex with LIG3 [9] that is required for LIG3 nuclear localization [10]. |
| GO:0071897 DNA biosynthetic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-based DNA biosynthetic process. Reason: Phosphodiester-bond formation completes DNA synthesis in replication and repair; true in a general sense, and LIG3 is the replicative ligase in mitochondria. The specific roles are captured by mitochondrial DNA replication and the repair terms. Supporting Evidence: PMID:21878356 These findings support the role of DNA ligase III as the replicative DNA ligase in human mtDNA replication |
| GO:0090298 negative regulation of mitochondrial DNA replication | IMP PMID:21878356 Involvement of DNA ligase III and ribonuclease H1 in mitocho... | MODIFY | Summary: Knockdown of LIG3 in cultured human cells attenuated recovery of mtDNA copy number after transient depletion and left nicks in replicating mtDNA, implicating LIG3 in Okazaki-fragment ligation. Reason: The data show that LIG3 is required for, and participates in, mtDNA replication (as the Okazaki-fragment ligase). The annotation to negative regulation inverts the sign of the knockdown result. Replace with mitochondrial DNA replication. Proposed replacements: mitochondrial DNA replication Supporting Evidence: PMID:21878356 DNA ligase III knockdown attenuated the recovery of mtDNA copy number and appeared to cause single strand nicks in replicating mtDNA molecules PMID:21878356 These findings support the role of DNA ligase III as the replicative DNA ligase in human mtDNA replication |
| GO:0090734 site of DNA damage | NAS PMID:33087283 XRCC1 - Strategies for coordinating and assembling a versati... | KEEP AS NON CORE | Summary: ComplexPortal NAS for site of DNA damage. Reason: LIG3:XRCC1 is recruited to SSB/BER and MMEJ sites; correct location for the repair activity, but peripheral to the definition of its function. Supporting Evidence: Reactome:R-HSA-5687673 The MRN complex recruits DNA ligase 3 (LIG3) bound to XRCC1 (LIG3:XRCC1) to microhomology-mediated end joining (MMEJ) sites |
| GO:0097681 double-strand break repair via alternative nonhomologous end joining | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA prediction of alternative NHEJ. Reason: LIG3/XRCC1 is the principal ligase of microhomology-biased alternative end joining, supported by extract fractionation, reconstitution with MRN, and mouse cell genetics (with LIG1 as a backup). Supporting Evidence: PMID:21816818 MRN interacts with DNA ligase IIIΞ±/XRCC1, stimulating intermolecular ligation, and together these proteins join incompatible DNA ends in a reaction that mimics alt-NHEJ. PMID:21655080 two alt-NHEJ pathways, one that is biased toward microhomology use and requires Lig3 PMID:15899791 These in vivo and in vitro observations identify DNA ligase III as a candidate component for B-NHEJ |
| GO:0000012 single strand break repair | IDA PMID:15744309 Defective DNA single-strand break repair in spinocerebellar ... | NEW | Summary: LIG3alpha, in complex with XRCC1, seals the nick at the end of single-strand break repair; TDP1 is recruited into SSBR complexes by direct interaction with LIG3alpha. Reason: LIG3 performs the ligation step of SSBR (participation, not merely requirement). XRCC1, the scaffold of the same complex, carries this term. Not covered by any existing row (BER is related but distinct). LIG1 can also seal SSBR intermediates, so the role is shared. Keyed as IDA to the experimental El-Khamisy et al. study, which isolated LIG3alpha-containing SSBR complexes from human cells (abstract only cached); the review article PMID:33087283 is kept as corroborating context. Supporting Evidence: PMID:33087283 The XRCC1 scaffold has been found to support two related DNA repair pathways: base excision repair (BER) and single-strand break repair (SSBR), while LIG3 participates in these and other pathways including nucleotide excision repair [3] and alternate non-homologous end joining (alt-NHEJ) [4]. PMID:15744309 We report that TDP1 is sequestered into multi-protein single-strand break repair (SSBR) complexes by direct interaction with DNA ligase IIIalpha |
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Download this section (compressed HTML)Q: In human cells, which nuclear repair events strictly require LIG3alpha rather than LIG1, given that nuclear Lig3 is dispensable for viability and for most XRCC1-dependent repair in mouse cells?
Q: Should the IMP row to negative regulation of mitochondrial DNA replication (PMID:21878356) be repointed to mitochondrial DNA replication? The paper shows LIG3 knockdown impairs mtDNA replication.
Experiment: Separation-of-function knock-ins in human cells that abolish either the mitochondrial (first ATG) or nuclear (second ATG) LIG3 isoform, with LIG1 depletion, to measure the contribution of nuclear LIG3alpha to SSBR, BER and microhomology-mediated end joining.
Type: genetic separation-of-function analysis
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