{"gene":"LIG1","run_date":"2026-04-28T18:30:27","timeline":{"discoveries":[{"year":2022,"finding":"Human LIG1 uses two PCNA-interacting motifs (PIPs) — one at its disordered N-terminus (PIPN-term) and one at its DNA-binding domain (PIPDBD) — to recruit PCNA to nicked DNA. Cryo-EM structures show LIG1 and PCNA assemble as two-stack rings encircling DNA; once assembled, PIPN-term is released and only PIPDBD is required for ligation, facilitating substrate handoff from FEN1. PCNA forms a toolbelt with FEN1 and nicked DNA and recruits LIG1 to an unoccupied monomer to drive the transfer of DNA to LIG1 during Okazaki fragment sealing.","method":"Cryo-EM structures combined with functional ligation assays and PIP-motif mutagenesis","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 1 — multiple cryo-EM structures with functional validation and mutagenesis in a single study","pmids":["36539424"],"is_preprint":false},{"year":2022,"finding":"X-ray structures of LIG1 bound to nick DNA containing G:T and A:C mismatches show that the LIG1 active site can accommodate a G:T wobble mismatch and transfer AMP to the 5'-phosphate (DNA-AMP intermediate), whereas an A:C mismatch stalls the reaction at the LIG1-AMP intermediate. APE1 interacts with LIG1 at the final BER steps and acts as a compensatory proofreading enzyme by removing mismatched bases.","method":"X-ray crystallography of LIG1/nick-DNA complexes, biochemical ligation assays, Co-IP/pull-down with APE1","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 1 — atomic structures plus functional biochemical assays in one study","pmids":["35790757"],"is_preprint":false},{"year":2021,"finding":"LIG1 syndrome mutations R771W and R641L disrupt a cooperative network of DNA-LIG1 interactions that couple DNA substrate engagement with productive Mg2+ cofactor binding required for catalysis. High-resolution X-ray structures and pre-steady-state kinetics show these mutations destabilize Mg2+ binding affinity and increase abortive ligation.","method":"X-ray crystallography, steady-state and pre-steady-state kinetics, active-site mutant characterization","journal":"Nucleic Acids Research","confidence":"High","confidence_rationale":"Tier 1 — structures combined with rigorous kinetic characterization and mutagenesis","pmids":["33444456"],"is_preprint":false},{"year":2019,"finding":"The UHRF1 tandem Tudor domain (TTD) binds the methylated histone-like region of DNA Ligase 1 (LIG1 K126me2/me3) with nanomolar affinity, permitting UHRF1 recruitment to chromatin; crystal structure of the UHRF1 TTD bound to a LIG1-K126me3 peptide reveals the structural basis for high-affinity binding and shows that phosphorylation can regulate this interaction. LIG1-K126me3 binding switches UHRF1 from a closed (auto-inhibited) to an open/flexible conformation.","method":"X-ray crystallography of UHRF1-TTD/LIG1-K126me3 peptide complex, binding affinity measurements, structural analysis of auto-inhibition relief","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with functional binding validation, mechanistic insight into UHRF1 regulation","pmids":["30639225"],"is_preprint":false},{"year":2024,"finding":"X-ray structures of LIG1 bound to 3'-RNA-DNA hybrid nicks (3'-rA:T and 3'-rG:C) reveal that residues Asp570 and Arg871 contact the 2'-OH of the ribose at the nick, and LIG1 forms a final phosphodiester bond with 3'-ribonucleotides as efficiently as with canonical deoxyribonucleotides in vitro, indicating a lack of sugar discrimination at the 3'-terminus.","method":"X-ray crystallography, in vitro nick-sealing assays","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 — multiple X-ray structures at different ligation steps plus biochemical assays","pmids":["38522520"],"is_preprint":false},{"year":2024,"finding":"X-ray structures of LIG1 bound to 5'-rG:C nick DNA at the initial ligation step reveal a large conformational change downstream of the nick and a shift at Arg871 in the adenylation domain; LIG1 discriminates against 5'-ribonucleotide-containing nicks (diminished ligation) compared to 3'-ribonucleotide-containing nicks (efficient ligation), establishing a sugar-discrimination mechanism specific to the 5'-end during ribonucleotide excision repair.","method":"X-ray crystallography, in vitro ligation assays with wild-type and active-site mutants","journal":"Journal of Biological Chemistry","confidence":"High","confidence_rationale":"Tier 1 — crystal structures combined with biochemical assays and mutagenesis","pmids":["39159820"],"is_preprint":false},{"year":2024,"finding":"Single-molecule fluorescence (C-Trap and TIRF) shows LIG1 full-length binds enriched at nick sites and exhibits 1D diffusion along DNA before forming a long-lived nick complex, whereas the C-terminal catalytic fragment binds non-specifically and more transiently; the N-terminal non-catalytic domain drives 1D diffusion and nick-site enrichment.","method":"Single-molecule fluorescence microscopy (C-Trap, TIRF), nick-binding assays with full-length and C-terminal truncation","journal":"Nucleic Acids Research","confidence":"High","confidence_rationale":"Tier 1 — two orthogonal single-molecule methods with domain-deletion controls","pmids":["39404052"],"is_preprint":false},{"year":2024,"finding":"Active-site residues F635 and F872 of LIG1 are required for mismatch discrimination: Ala/Leu substitutions at these positions abolish ligation of all 12 non-canonical mismatched nick substrates. Structures of F635A and F872A mutants reveal that these residues govern DNA end rigidity and the alignment of the 5'-end of the nick, creating a barrier to adenylate transfer in the presence of mismatches.","method":"X-ray crystallography of LIG1 active-site mutants with mismatch-containing nick DNA, biochemical ligation assays","journal":"bioRxiv (preprint, later published)","confidence":"High","confidence_rationale":"Tier 1 — crystal structures plus comprehensive biochemical mutagenesis panel","pmids":["39574773"],"is_preprint":true},{"year":2024,"finding":"LIG1 forms X-ray crystal structure complexes with 3'-8-oxodG and 3'-8-oxorG nicks opposite C or A, capturing pre- and post-catalytic ligation steps. The ligase active site accommodates oxidative lesions via shifts in template base position depending on 8-oxoG Hoogsteen vs. Watson-Crick conformation, leading to mutagenic or non-mutagenic ligation. LIG1 and LIG3α seal nicks after polβ insertion of 8-oxorGTP:A, and APE1 can clean oxidatively damaged ends.","method":"X-ray crystallography, in vitro ligation assays with wild-type and variant enzymes","journal":"bioRxiv (preprint)","confidence":"High","confidence_rationale":"Tier 1 — multiple crystal structures at distinct catalytic steps plus biochemical assays","pmids":["38766188"],"is_preprint":true},{"year":2024,"finding":"Unfilled gaps by polβ result in gap ligation by LIG1, forming single-nucleotide deletion products. LIG1 cannot discriminate against nick DNA containing a 3'-ribonucleotide regardless of base-pairing potential; APE1 has distinct exonuclease specificity for removing 3'-mismatched bases and ribonucleotides at the nick.","method":"In vitro gap-filling and nick-sealing assays with polβ and LIG1, ribonucleotide substitution experiments, APE1 exonuclease assays","journal":"Nucleic Acids Research","confidence":"High","confidence_rationale":"Tier 1 — reconstituted multi-enzyme BER assays with defined substrates and mutagenesis","pmids":["38366780"],"is_preprint":false},{"year":2025,"finding":"The HD-associated LIG1 K845N variant shows reduced ligation efficiency for nicks with mismatches, 8-oxoG, and damaged ends; crystal structures show differences in distances between the K/N845 side chain and DNA ends; single-molecule TIRF reveals K845N binds less frequently to nick sites, indicating diminished nick affinity, consistent with impaired nick recognition.","method":"X-ray crystallography, pre-steady-state kinetics, TIRF single-molecule microscopy","journal":"NAR Molecular Medicine","confidence":"High","confidence_rationale":"Tier 1 — crystal structures plus kinetics plus single-molecule measurements","pmids":["41346861"],"is_preprint":false},{"year":2025,"finding":"In vitro ligase assays demonstrate that the K845N HD-modifier variant of LIG1 enhances discrimination toward mismatched substrates and increases ligation fidelity. In cell-based assays, K845N confers protection against oxidative stress. In vivo, the mouse ortholog (K843N) suppresses somatic CAG repeat expansion in HD knock-in mice.","method":"In vitro ligation kinetics, cell-based oxidative stress assays, HD knock-in mouse model","journal":"Proceedings of the National Academy of Sciences","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro reconstitution with kinetics, cellular assays, and in vivo mouse model","pmids":["41770933"],"is_preprint":false},{"year":2025,"finding":"X-ray structures of LIG1 with 3'-8-oxodG and 3'-8-oxorG nick substrates templating A or C show structural adjustments at the +1 and +2 nucleotide positions and template base shifts depending on the dual coding potential (Hoogsteen vs. Watson-Crick) of 8-oxoG. These differences lead to mutagenic or non-mutagenic nick sealing by LIG1.","method":"X-ray crystallography, in vitro ligation assays","journal":"Nucleic Acids Research","confidence":"High","confidence_rationale":"Tier 1 — crystal structures at multiple ligation steps with biochemical validation","pmids":["41370201"],"is_preprint":false},{"year":2025,"finding":"LIG1 inactivation (via CRISPRn, CRISPRi, RNAi, and targeted protein degradation) causes viability loss selectively in BRCA1-mutant cells in vitro and in vivo. This synthetic lethality requires LIG1 catalytic activity (catalytically dead K568A does not rescue), and LIG1 perturbation increases PAR staining consistent with accumulation of ssDNA nicks. CRISPR/Cas9 screens also identified LIG1 loss as a PARP inhibitor sensitizer, causing replication stress and DNA double-strand breaks.","method":"CRISPR/Cas9 genetic screens, multiple LIG1 depletion strategies with catalytic mutant rescue, PAR staining, xenograft in vivo model","journal":"Molecular Cancer Therapeutics / Journal of Clinical Investigation","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal loss-of-function approaches with mechanistic rescue and in vivo confirmation","pmids":["39868490","39718835"],"is_preprint":false},{"year":2018,"finding":"SRSF1 binds to LIG1 mRNA and stabilizes it while also enhancing its translation in an mTOR-dependent manner, thereby increasing LIG1 protein levels in NSCLC cells. siRNA-mediated LIG1 knockdown reduces NSCLC cell proliferation and increases apoptosis.","method":"RNA-binding protein immunoprecipitation, mRNA stability assays, mTOR inhibition, siRNA knockdown with phenotypic readout","journal":"Laboratory Investigation","confidence":"Medium","confidence_rationale":"Tier 2–3 — RIP and functional assays establish post-transcriptional regulation, but limited mechanistic depth","pmids":["30181552"],"is_preprint":false},{"year":2025,"finding":"During Okazaki fragment maturation, Polδ, FEN1, and LIG1 sequentially but not simultaneously bind PCNA. FEN1 R192 methylation mediates its PCNA association and prevents premature LIG1 loading; JMJD1B-mediated demethylation of FEN1 R192 promotes FEN1 dissociation from PCNA and enables LIG1 recruitment for nick ligation.","method":"Cell-based co-immunoprecipitation, methylation mutant analysis, JMJD1B knockout cells, replication intermediate analysis","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 2 — genetic and biochemical evidence in mammalian cells, mechanistic model supported by multiple mutants; preprint only","pmids":["bio_10.1101_2025.10.06.680735"],"is_preprint":true},{"year":2025,"finding":"Single-molecule TIRF shows LIG3α binds less frequently but forms longer-lived complexes than LIG1 on nick DNA; both ligases can bind gap DNA as efficiently as nick DNA, but LIG1 forms more stable long-lived complexes on gap DNA compared to LIG3α, revealing distinct nick vs. gap substrate recognition dynamics between the two ligases.","method":"Single-molecule TIRF microscopy, in vitro ligation assays comparing LIG1 and LIG3α","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 2 — single-molecule approach with direct comparison; preprint only","pmids":["40666977"],"is_preprint":true}],"current_model":"Human DNA Ligase I (LIG1) is the main replicative ligase that seals Okazaki fragments and completes DNA repair pathways by catalyzing phosphodiester bond formation at nicked DNA in three AMP-dependent steps; it uses two PCNA-interacting motifs to form a toolbelt with PCNA and FEN1 on lagging-strand DNA, discriminates against mismatches through a cooperative network of DNA–metal interactions involving active-site residues F635 and F872 and Mg2+ cofactors, is recruited to chromatin via its methylated K126 region binding the UHRF1 tandem Tudor domain, searches for nick sites by 1D diffusion facilitated by its N-terminal domain, and is tightly coordinated with polβ and APE1 in base excision repair to ensure faithful nick sealing while avoiding mutagenic ligation of mismatched, oxidized, or ribonucleotide-containing repair intermediates."},"narrative":{"teleology":[{"year":2018,"claim":"How LIG1 protein levels are controlled post-transcriptionally was unknown; SRSF1 was shown to bind and stabilize LIG1 mRNA while promoting its mTOR-dependent translation, linking LIG1 abundance to growth signaling in cancer cells.","evidence":"RNA immunoprecipitation, mRNA stability assays, and mTOR inhibition in NSCLC cells","pmids":["30181552"],"confidence":"Medium","gaps":["Limited mechanistic depth on SRSF1-LIG1 mRNA binding specificity","No direct in vivo validation of mTOR-dependent LIG1 regulation","Other post-transcriptional regulators of LIG1 not explored"]},{"year":2019,"claim":"The mechanism by which LIG1 connects to chromatin maintenance machinery was unclear; structural and biophysical studies revealed that UHRF1's tandem Tudor domain binds LIG1-K126me2/me3 with nanomolar affinity, switching UHRF1 from an auto-inhibited to an open conformation and thereby recruiting UHRF1 to chromatin.","evidence":"X-ray crystallography of UHRF1-TTD/LIG1-K126me3 peptide complex with binding affinity measurements","pmids":["30639225"],"confidence":"High","gaps":["Functional consequence of this interaction for DNA methylation maintenance in cells not fully established","Writers/erasers of K126 methylation not identified in this study"]},{"year":2021,"claim":"How disease-causing LIG1 mutations impair catalysis was unknown; structural and kinetic analysis of the LIG1 syndrome variants R771W and R641L revealed they disrupt a cooperative network coupling DNA engagement to productive Mg²⁺ binding, increasing abortive ligation.","evidence":"X-ray crystallography combined with pre-steady-state and steady-state kinetics of active-site mutants","pmids":["33444456"],"confidence":"High","gaps":["Whether compensatory repair pathways mitigate these defects in patient cells not addressed","Structural basis for other LIG1 syndrome mutations not yet determined"]},{"year":2022,"claim":"How LIG1 coordinates with PCNA and FEN1 during Okazaki fragment maturation was structurally undefined; cryo-EM structures showed LIG1 uses two PIP motifs to recruit PCNA to nicked DNA as stacked rings, with PIPN-term released after assembly so that PCNA forms a toolbelt with FEN1 to hand off the nick substrate to LIG1.","evidence":"Cryo-EM structures with PIP-motif mutagenesis and functional ligation assays","pmids":["36539424"],"confidence":"High","gaps":["Dynamics of the handoff in the cellular context not captured","Role of post-translational modifications on PIP motifs not explored"]},{"year":2022,"claim":"Whether LIG1 has intrinsic mismatch discrimination and how APE1 compensates was unclear; X-ray structures showed LIG1 accommodates a G:T wobble mismatch (reaching DNA-AMP) but stalls on A:C mismatches (remaining at LIG1-AMP), and APE1 was shown to interact with LIG1 and proofread mismatched nick ends.","evidence":"X-ray crystallography of LIG1/mismatch-nick complexes, biochemical assays, and APE1 co-immunoprecipitation","pmids":["35790757"],"confidence":"High","gaps":["Structural basis of the APE1-LIG1 physical interface not resolved","Contribution of mismatch discrimination in vivo not quantified"]},{"year":2024,"claim":"How LIG1 handles ribonucleotide-containing nicks during ribonucleotide excision repair was unknown; structural and biochemical studies established that LIG1 efficiently seals 3′-ribonucleotide nicks (Asp570/Arg871 contact the 2′-OH) but discriminates against 5′-ribonucleotide nicks via conformational rearrangements at Arg871, defining an asymmetric sugar-selectivity mechanism.","evidence":"X-ray crystallography of LIG1 with 3′- and 5′-RNA-DNA hybrid nick substrates, in vitro nick-sealing assays with active-site mutants","pmids":["38522520","39159820"],"confidence":"High","gaps":["In vivo relevance of asymmetric sugar discrimination for genome stability not tested","Whether LIG3α shares this asymmetry not determined"]},{"year":2024,"claim":"The specific active-site determinants of LIG1 mismatch fidelity were undefined; mutagenesis and structures of F635A and F872A mutants demonstrated these residues enforce DNA end rigidity and 5′-end alignment at the nick, creating a barrier to adenylate transfer on all 12 non-canonical mismatches.","evidence":"X-ray crystallography of LIG1 F635/F872 mutants with mismatched nick DNA, comprehensive biochemical ligation panel","pmids":["39574773"],"confidence":"High","gaps":["Preprint at time of discovery; awaits formal peer review","Whether these residues also govern discrimination against damaged bases not fully explored"]},{"year":2024,"claim":"How LIG1 locates nick sites along DNA was unknown; single-molecule imaging revealed that the N-terminal non-catalytic domain enables one-dimensional diffusion along DNA before forming long-lived complexes at nicks, whereas the catalytic core alone binds non-specifically and transiently.","evidence":"Single-molecule TIRF and C-Trap fluorescence microscopy with full-length versus C-terminal truncation constructs","pmids":["39404052"],"confidence":"High","gaps":["Whether PCNA or other replication factors modulate 1D diffusion not tested","In vivo diffusion parameters not measured"]},{"year":2024,"claim":"How LIG1 handles oxidative lesions inserted by pol β during BER was structurally unresolved; crystal structures captured LIG1 at pre- and post-catalytic steps with 3′-8-oxodG/8-oxorG nicks, revealing that Hoogsteen versus Watson-Crick pairing of 8-oxoG determines mutagenic or non-mutagenic ligation outcomes, and that APE1 can excise oxidatively damaged ends to limit mutagenic sealing.","evidence":"X-ray crystallography of LIG1 with 8-oxoG-containing nick substrates, in vitro ligation assays","pmids":["38766188","41370201"],"confidence":"High","gaps":["Cellular frequency of mutagenic versus non-mutagenic ligation of 8-oxoG nicks not quantified","Contribution of LIG3α to 8-oxoG nick ligation in BER not compared"]},{"year":2024,"claim":"Whether LIG1 is a therapeutic vulnerability in homologous recombination-deficient cancers was untested; multiple orthogonal depletion strategies demonstrated that LIG1 loss causes selective lethality in BRCA1-mutant cells through accumulation of single-strand breaks and replication stress, establishing LIG1 as a synthetic lethal target.","evidence":"CRISPR screens, CRISPRi, RNAi, targeted protein degradation, catalytic-dead rescue (K568A), PAR staining, xenograft models","pmids":["39868490","39718835"],"confidence":"High","gaps":["Whether LIG1 inhibition synergizes with PARP inhibitors in clinical contexts not established","Mechanism of synthetic lethality beyond nick accumulation not fully dissected"]},{"year":2025,"claim":"The functional impact of the Huntington's disease-associated LIG1 K845N variant was unknown; structural, kinetic, and in vivo studies showed K845N reduces nick affinity and enhances mismatch discrimination, conferring protection against oxidative stress in cells and suppressing somatic CAG repeat expansion in HD knock-in mice.","evidence":"X-ray crystallography, pre-steady-state kinetics, TIRF single-molecule microscopy, cell-based oxidative stress assays, HD knock-in mouse model","pmids":["41346861","41770933"],"confidence":"High","gaps":["Whether K845N affects replicative ligation efficiency in vivo not fully addressed","Mechanism by which enhanced fidelity suppresses repeat expansion at the molecular level not fully defined"]},{"year":null,"claim":"Key unresolved questions include: the structural basis of the APE1-LIG1 physical interaction; how post-translational modifications (beyond K126 methylation) regulate LIG1 activity and recruitment in vivo; and whether LIG1's 1D diffusion mechanism operates in the chromatin context and is modulated by replication/repair factors.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure of an APE1-LIG1 complex","In vivo regulation of LIG1 by PTMs beyond K126me largely unexplored","Chromatin-context single-molecule studies of LIG1 not performed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[0,1,2,4,5,7,9,10,11,12]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,1,4,5,6,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,13]},{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[0,15]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[1,2,4,5,8,9,10,11,12]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[2,10,11,13]}],"complexes":["PCNA-FEN1-LIG1 toolbelt"],"partners":["PCNA","FEN1","APE1","UHRF1","POLB","SRSF1"],"other_free_text":[]},"mechanistic_narrative":"LIG1 is the principal replicative DNA ligase in human cells, sealing Okazaki fragments during lagging-strand synthesis and completing nick ligation in base excision repair (BER) and ribonucleotide excision repair pathways. It catalyzes phosphodiester bond formation through a three-step AMP-dependent mechanism, using two PCNA-interacting motifs to assemble a toolbelt complex with PCNA and FEN1 on nicked DNA—where PIPN-term mediates initial recruitment and PIPDBD sustains ligation, enabling substrate handoff from FEN1 [PMID:36539424]—while its N-terminal non-catalytic domain drives one-dimensional diffusion along DNA to locate nick sites [PMID:39404052]. LIG1 discriminates against aberrant substrates through active-site residues F635 and F872 that enforce DNA end rigidity to block mismatch ligation [PMID:39574773], a cooperative network coupling DNA engagement to Mg²⁺ cofactor binding [PMID:33444456], and asymmetric sugar selectivity that permits 3′-ribonucleotide but rejects 5′-ribonucleotide nick sealing [PMID:38522520, PMID:39159820]; APE1 acts as a compensatory proofreader removing mismatched or damaged 3′-ends that escape this fidelity checkpoint [PMID:35790757, PMID:38366780]. LIG1 catalytic activity is selectively essential in BRCA1-deficient cells, where its loss causes accumulation of single-strand breaks, replication stress, and synthetic lethality both in vitro and in vivo [PMID:39868490, PMID:39718835], and the Huntington's disease-modifier variant K845N enhances mismatch discrimination and suppresses somatic CAG repeat expansion in HD knock-in mice [PMID:41770933]."},"prefetch_data":{"uniprot":{"accession":"P18858","full_name":"DNA ligase 1","aliases":["DNA ligase I","Polydeoxyribonucleotide synthase [ATP] 1"],"length_aa":919,"mass_kda":101.7,"function":"DNA ligase that seals nicks in double-stranded during DNA repair (PubMed:30395541). Also involved in DNA replication and DNA recombination","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P18858/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LIG1","classification":"Not Classified","n_dependent_lines":269,"n_total_lines":1208,"dependency_fraction":0.222682119205298},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000105486","cell_line_id":"CID000810","localizations":[{"compartment":"nuclear_punctae","grade":3},{"compartment":"nucleoplasm","grade":3}],"interactors":[{"gene":"UBE3B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000810","total_profiled":1310},"omim":[{"mim_id":"619774","title":"IMMUNODEFICIENCY 96; IMD96","url":"https://www.omim.org/entry/619774"},{"mim_id":"608868","title":"LEUCINE-RICH REPEATS- AND IMMUNOGLOBULIN-LIKE DOMAINS-CONTAINING PROTEIN 1; LRIG1","url":"https://www.omim.org/entry/608868"},{"mim_id":"602450","title":"SEVERE COMBINED IMMUNODEFICIENCY WITH SENSITIVITY TO IONIZING RADIATION","url":"https://www.omim.org/entry/602450"},{"mim_id":"600940","title":"LIGASE III, DNA, ATP-DEPENDENT; LIG3","url":"https://www.omim.org/entry/600940"},{"mim_id":"276700","title":"TYROSINEMIA, TYPE I; TYRSN1","url":"https://www.omim.org/entry/276700"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Golgi apparatus","reliability":"Additional"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"bone marrow","ntpm":29.1},{"tissue":"lymphoid tissue","ntpm":20.3}],"url":"https://www.proteinatlas.org/search/LIG1"},"hgnc":{"alias_symbol":["LIGI","hLig1"],"prev_symbol":[]},"alphafold":{"accession":"Q96JA1","domains":[{"cath_id":"3.80.10.10","chopping":"320-491","consensus_level":"medium","plddt":93.783,"start":320,"end":491},{"cath_id":"2.60.40.10","chopping":"509-582","consensus_level":"high","plddt":87.1378,"start":509,"end":582},{"cath_id":"2.60.40.10","chopping":"605-690","consensus_level":"high","plddt":88.0147,"start":605,"end":690},{"cath_id":"2.60.40.10","chopping":"699-782","consensus_level":"high","plddt":90.7639,"start":699,"end":782}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JA1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JA1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JA1-F1-predicted_aligned_error_v6.png","plddt_mean":74.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LIG1","jax_strain_url":"https://www.jax.org/strain/search?query=LIG1"},"sequence":{"accession":"Q96JA1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96JA1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96JA1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JA1"}},"corpus_meta":[{"pmid":"11414704","id":"PMC_11414704","title":"Cloning, characterization, and expression of human LIG1.","date":"2001","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/11414704","citation_count":119,"is_preprint":false},{"pmid":"12067728","id":"PMC_12067728","title":"Targeted disruption of LIG-1 gene results in psoriasiform epidermal hyperplasia.","date":"2002","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/12067728","citation_count":96,"is_preprint":false},{"pmid":"8798419","id":"PMC_8798419","title":"cDNA cloning of a novel membrane glycoprotein that is expressed specifically in glial cells in the mouse brain. LIG-1, a protein with leucine-rich repeats and immunoglobulin-like domains.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8798419","citation_count":72,"is_preprint":false},{"pmid":"30639225","id":"PMC_30639225","title":"Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.","date":"2019","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/30639225","citation_count":48,"is_preprint":false},{"pmid":"38044421","id":"PMC_38044421","title":"hsa_circ_0007919 induces LIG1 transcription by binding to FOXA1/TET1 to enhance the DNA damage response and promote gemcitabine resistance in pancreatic ductal adenocarcinoma.","date":"2023","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38044421","citation_count":44,"is_preprint":false},{"pmid":"21781197","id":"PMC_21781197","title":"Arabidopsis ARP endonuclease 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Cryo-EM structures show LIG1 and PCNA assemble as two-stack rings encircling DNA; once assembled, PIPN-term is released and only PIPDBD is required for ligation, facilitating substrate handoff from FEN1. PCNA forms a toolbelt with FEN1 and nicked DNA and recruits LIG1 to an unoccupied monomer to drive the transfer of DNA to LIG1 during Okazaki fragment sealing.\",\n      \"method\": \"Cryo-EM structures combined with functional ligation assays and PIP-motif mutagenesis\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple cryo-EM structures with functional validation and mutagenesis in a single study\",\n      \"pmids\": [\"36539424\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"X-ray structures of LIG1 bound to nick DNA containing G:T and A:C mismatches show that the LIG1 active site can accommodate a G:T wobble mismatch and transfer AMP to the 5'-phosphate (DNA-AMP intermediate), whereas an A:C mismatch stalls the reaction at the LIG1-AMP intermediate. APE1 interacts with LIG1 at the final BER steps and acts as a compensatory proofreading enzyme by removing mismatched bases.\",\n      \"method\": \"X-ray crystallography of LIG1/nick-DNA complexes, biochemical ligation assays, Co-IP/pull-down with APE1\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — atomic structures plus functional biochemical assays in one study\",\n      \"pmids\": [\"35790757\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"LIG1 syndrome mutations R771W and R641L disrupt a cooperative network of DNA-LIG1 interactions that couple DNA substrate engagement with productive Mg2+ cofactor binding required for catalysis. High-resolution X-ray structures and pre-steady-state kinetics show these mutations destabilize Mg2+ binding affinity and increase abortive ligation.\",\n      \"method\": \"X-ray crystallography, steady-state and pre-steady-state kinetics, active-site mutant characterization\",\n      \"journal\": \"Nucleic Acids Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — structures combined with rigorous kinetic characterization and mutagenesis\",\n      \"pmids\": [\"33444456\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The UHRF1 tandem Tudor domain (TTD) binds the methylated histone-like region of DNA Ligase 1 (LIG1 K126me2/me3) with nanomolar affinity, permitting UHRF1 recruitment to chromatin; crystal structure of the UHRF1 TTD bound to a LIG1-K126me3 peptide reveals the structural basis for high-affinity binding and shows that phosphorylation can regulate this interaction. LIG1-K126me3 binding switches UHRF1 from a closed (auto-inhibited) to an open/flexible conformation.\",\n      \"method\": \"X-ray crystallography of UHRF1-TTD/LIG1-K126me3 peptide complex, binding affinity measurements, structural analysis of auto-inhibition relief\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with functional binding validation, mechanistic insight into UHRF1 regulation\",\n      \"pmids\": [\"30639225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"X-ray structures of LIG1 bound to 3'-RNA-DNA hybrid nicks (3'-rA:T and 3'-rG:C) reveal that residues Asp570 and Arg871 contact the 2'-OH of the ribose at the nick, and LIG1 forms a final phosphodiester bond with 3'-ribonucleotides as efficiently as with canonical deoxyribonucleotides in vitro, indicating a lack of sugar discrimination at the 3'-terminus.\",\n      \"method\": \"X-ray crystallography, in vitro nick-sealing assays\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple X-ray structures at different ligation steps plus biochemical assays\",\n      \"pmids\": [\"38522520\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"X-ray structures of LIG1 bound to 5'-rG:C nick DNA at the initial ligation step reveal a large conformational change downstream of the nick and a shift at Arg871 in the adenylation domain; LIG1 discriminates against 5'-ribonucleotide-containing nicks (diminished ligation) compared to 3'-ribonucleotide-containing nicks (efficient ligation), establishing a sugar-discrimination mechanism specific to the 5'-end during ribonucleotide excision repair.\",\n      \"method\": \"X-ray crystallography, in vitro ligation assays with wild-type and active-site mutants\",\n      \"journal\": \"Journal of Biological Chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures combined with biochemical assays and mutagenesis\",\n      \"pmids\": [\"39159820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Single-molecule fluorescence (C-Trap and TIRF) shows LIG1 full-length binds enriched at nick sites and exhibits 1D diffusion along DNA before forming a long-lived nick complex, whereas the C-terminal catalytic fragment binds non-specifically and more transiently; the N-terminal non-catalytic domain drives 1D diffusion and nick-site enrichment.\",\n      \"method\": \"Single-molecule fluorescence microscopy (C-Trap, TIRF), nick-binding assays with full-length and C-terminal truncation\",\n      \"journal\": \"Nucleic Acids Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — two orthogonal single-molecule methods with domain-deletion controls\",\n      \"pmids\": [\"39404052\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Active-site residues F635 and F872 of LIG1 are required for mismatch discrimination: Ala/Leu substitutions at these positions abolish ligation of all 12 non-canonical mismatched nick substrates. Structures of F635A and F872A mutants reveal that these residues govern DNA end rigidity and the alignment of the 5'-end of the nick, creating a barrier to adenylate transfer in the presence of mismatches.\",\n      \"method\": \"X-ray crystallography of LIG1 active-site mutants with mismatch-containing nick DNA, biochemical ligation assays\",\n      \"journal\": \"bioRxiv (preprint, later published)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures plus comprehensive biochemical mutagenesis panel\",\n      \"pmids\": [\"39574773\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LIG1 forms X-ray crystal structure complexes with 3'-8-oxodG and 3'-8-oxorG nicks opposite C or A, capturing pre- and post-catalytic ligation steps. The ligase active site accommodates oxidative lesions via shifts in template base position depending on 8-oxoG Hoogsteen vs. Watson-Crick conformation, leading to mutagenic or non-mutagenic ligation. LIG1 and LIG3α seal nicks after polβ insertion of 8-oxorGTP:A, and APE1 can clean oxidatively damaged ends.\",\n      \"method\": \"X-ray crystallography, in vitro ligation assays with wild-type and variant enzymes\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple crystal structures at distinct catalytic steps plus biochemical assays\",\n      \"pmids\": [\"38766188\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Unfilled gaps by polβ result in gap ligation by LIG1, forming single-nucleotide deletion products. LIG1 cannot discriminate against nick DNA containing a 3'-ribonucleotide regardless of base-pairing potential; APE1 has distinct exonuclease specificity for removing 3'-mismatched bases and ribonucleotides at the nick.\",\n      \"method\": \"In vitro gap-filling and nick-sealing assays with polβ and LIG1, ribonucleotide substitution experiments, APE1 exonuclease assays\",\n      \"journal\": \"Nucleic Acids Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted multi-enzyme BER assays with defined substrates and mutagenesis\",\n      \"pmids\": [\"38366780\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The HD-associated LIG1 K845N variant shows reduced ligation efficiency for nicks with mismatches, 8-oxoG, and damaged ends; crystal structures show differences in distances between the K/N845 side chain and DNA ends; single-molecule TIRF reveals K845N binds less frequently to nick sites, indicating diminished nick affinity, consistent with impaired nick recognition.\",\n      \"method\": \"X-ray crystallography, pre-steady-state kinetics, TIRF single-molecule microscopy\",\n      \"journal\": \"NAR Molecular Medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures plus kinetics plus single-molecule measurements\",\n      \"pmids\": [\"41346861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In vitro ligase assays demonstrate that the K845N HD-modifier variant of LIG1 enhances discrimination toward mismatched substrates and increases ligation fidelity. In cell-based assays, K845N confers protection against oxidative stress. In vivo, the mouse ortholog (K843N) suppresses somatic CAG repeat expansion in HD knock-in mice.\",\n      \"method\": \"In vitro ligation kinetics, cell-based oxidative stress assays, HD knock-in mouse model\",\n      \"journal\": \"Proceedings of the National Academy of Sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro reconstitution with kinetics, cellular assays, and in vivo mouse model\",\n      \"pmids\": [\"41770933\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"X-ray structures of LIG1 with 3'-8-oxodG and 3'-8-oxorG nick substrates templating A or C show structural adjustments at the +1 and +2 nucleotide positions and template base shifts depending on the dual coding potential (Hoogsteen vs. Watson-Crick) of 8-oxoG. These differences lead to mutagenic or non-mutagenic nick sealing by LIG1.\",\n      \"method\": \"X-ray crystallography, in vitro ligation assays\",\n      \"journal\": \"Nucleic Acids Research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structures at multiple ligation steps with biochemical validation\",\n      \"pmids\": [\"41370201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LIG1 inactivation (via CRISPRn, CRISPRi, RNAi, and targeted protein degradation) causes viability loss selectively in BRCA1-mutant cells in vitro and in vivo. This synthetic lethality requires LIG1 catalytic activity (catalytically dead K568A does not rescue), and LIG1 perturbation increases PAR staining consistent with accumulation of ssDNA nicks. CRISPR/Cas9 screens also identified LIG1 loss as a PARP inhibitor sensitizer, causing replication stress and DNA double-strand breaks.\",\n      \"method\": \"CRISPR/Cas9 genetic screens, multiple LIG1 depletion strategies with catalytic mutant rescue, PAR staining, xenograft in vivo model\",\n      \"journal\": \"Molecular Cancer Therapeutics / Journal of Clinical Investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal loss-of-function approaches with mechanistic rescue and in vivo confirmation\",\n      \"pmids\": [\"39868490\", \"39718835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SRSF1 binds to LIG1 mRNA and stabilizes it while also enhancing its translation in an mTOR-dependent manner, thereby increasing LIG1 protein levels in NSCLC cells. siRNA-mediated LIG1 knockdown reduces NSCLC cell proliferation and increases apoptosis.\",\n      \"method\": \"RNA-binding protein immunoprecipitation, mRNA stability assays, mTOR inhibition, siRNA knockdown with phenotypic readout\",\n      \"journal\": \"Laboratory Investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — RIP and functional assays establish post-transcriptional regulation, but limited mechanistic depth\",\n      \"pmids\": [\"30181552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"During Okazaki fragment maturation, Polδ, FEN1, and LIG1 sequentially but not simultaneously bind PCNA. FEN1 R192 methylation mediates its PCNA association and prevents premature LIG1 loading; JMJD1B-mediated demethylation of FEN1 R192 promotes FEN1 dissociation from PCNA and enables LIG1 recruitment for nick ligation.\",\n      \"method\": \"Cell-based co-immunoprecipitation, methylation mutant analysis, JMJD1B knockout cells, replication intermediate analysis\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic and biochemical evidence in mammalian cells, mechanistic model supported by multiple mutants; preprint only\",\n      \"pmids\": [\"bio_10.1101_2025.10.06.680735\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Single-molecule TIRF shows LIG3α binds less frequently but forms longer-lived complexes than LIG1 on nick DNA; both ligases can bind gap DNA as efficiently as nick DNA, but LIG1 forms more stable long-lived complexes on gap DNA compared to LIG3α, revealing distinct nick vs. gap substrate recognition dynamics between the two ligases.\",\n      \"method\": \"Single-molecule TIRF microscopy, in vitro ligation assays comparing LIG1 and LIG3α\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — single-molecule approach with direct comparison; preprint only\",\n      \"pmids\": [\"40666977\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"Human DNA Ligase I (LIG1) is the main replicative ligase that seals Okazaki fragments and completes DNA repair pathways by catalyzing phosphodiester bond formation at nicked DNA in three AMP-dependent steps; it uses two PCNA-interacting motifs to form a toolbelt with PCNA and FEN1 on lagging-strand DNA, discriminates against mismatches through a cooperative network of DNA–metal interactions involving active-site residues F635 and F872 and Mg2+ cofactors, is recruited to chromatin via its methylated K126 region binding the UHRF1 tandem Tudor domain, searches for nick sites by 1D diffusion facilitated by its N-terminal domain, and is tightly coordinated with polβ and APE1 in base excision repair to ensure faithful nick sealing while avoiding mutagenic ligation of mismatched, oxidized, or ribonucleotide-containing repair intermediates.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"LIG1 is the principal replicative DNA ligase in human cells, sealing Okazaki fragments during lagging-strand synthesis and completing nick ligation in base excision repair (BER) and ribonucleotide excision repair pathways. It catalyzes phosphodiester bond formation through a three-step AMP-dependent mechanism, using two PCNA-interacting motifs to assemble a toolbelt complex with PCNA and FEN1 on nicked DNA—where PIPN-term mediates initial recruitment and PIPDBD sustains ligation, enabling substrate handoff from FEN1 [PMID:36539424]—while its N-terminal non-catalytic domain drives one-dimensional diffusion along DNA to locate nick sites [PMID:39404052]. LIG1 discriminates against aberrant substrates through active-site residues F635 and F872 that enforce DNA end rigidity to block mismatch ligation [PMID:39574773], a cooperative network coupling DNA engagement to Mg²⁺ cofactor binding [PMID:33444456], and asymmetric sugar selectivity that permits 3′-ribonucleotide but rejects 5′-ribonucleotide nick sealing [PMID:38522520, PMID:39159820]; APE1 acts as a compensatory proofreader removing mismatched or damaged 3′-ends that escape this fidelity checkpoint [PMID:35790757, PMID:38366780]. LIG1 catalytic activity is selectively essential in BRCA1-deficient cells, where its loss causes accumulation of single-strand breaks, replication stress, and synthetic lethality both in vitro and in vivo [PMID:39868490, PMID:39718835], and the Huntington's disease-modifier variant K845N enhances mismatch discrimination and suppresses somatic CAG repeat expansion in HD knock-in mice [PMID:41770933].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"How LIG1 protein levels are controlled post-transcriptionally was unknown; SRSF1 was shown to bind and stabilize LIG1 mRNA while promoting its mTOR-dependent translation, linking LIG1 abundance to growth signaling in cancer cells.\",\n      \"evidence\": \"RNA immunoprecipitation, mRNA stability assays, and mTOR inhibition in NSCLC cells\",\n      \"pmids\": [\"30181552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Limited mechanistic depth on SRSF1-LIG1 mRNA binding specificity\", \"No direct in vivo validation of mTOR-dependent LIG1 regulation\", \"Other post-transcriptional regulators of LIG1 not explored\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The mechanism by which LIG1 connects to chromatin maintenance machinery was unclear; structural and biophysical studies revealed that UHRF1's tandem Tudor domain binds LIG1-K126me2/me3 with nanomolar affinity, switching UHRF1 from an auto-inhibited to an open conformation and thereby recruiting UHRF1 to chromatin.\",\n      \"evidence\": \"X-ray crystallography of UHRF1-TTD/LIG1-K126me3 peptide complex with binding affinity measurements\",\n      \"pmids\": [\"30639225\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of this interaction for DNA methylation maintenance in cells not fully established\", \"Writers/erasers of K126 methylation not identified in this study\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"How disease-causing LIG1 mutations impair catalysis was unknown; structural and kinetic analysis of the LIG1 syndrome variants R771W and R641L revealed they disrupt a cooperative network coupling DNA engagement to productive Mg²⁺ binding, increasing abortive ligation.\",\n      \"evidence\": \"X-ray crystallography combined with pre-steady-state and steady-state kinetics of active-site mutants\",\n      \"pmids\": [\"33444456\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether compensatory repair pathways mitigate these defects in patient cells not addressed\", \"Structural basis for other LIG1 syndrome mutations not yet determined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"How LIG1 coordinates with PCNA and FEN1 during Okazaki fragment maturation was structurally undefined; cryo-EM structures showed LIG1 uses two PIP motifs to recruit PCNA to nicked DNA as stacked rings, with PIPN-term released after assembly so that PCNA forms a toolbelt with FEN1 to hand off the nick substrate to LIG1.\",\n      \"evidence\": \"Cryo-EM structures with PIP-motif mutagenesis and functional ligation assays\",\n      \"pmids\": [\"36539424\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics of the handoff in the cellular context not captured\", \"Role of post-translational modifications on PIP motifs not explored\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether LIG1 has intrinsic mismatch discrimination and how APE1 compensates was unclear; X-ray structures showed LIG1 accommodates a G:T wobble mismatch (reaching DNA-AMP) but stalls on A:C mismatches (remaining at LIG1-AMP), and APE1 was shown to interact with LIG1 and proofread mismatched nick ends.\",\n      \"evidence\": \"X-ray crystallography of LIG1/mismatch-nick complexes, biochemical assays, and APE1 co-immunoprecipitation\",\n      \"pmids\": [\"35790757\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the APE1-LIG1 physical interface not resolved\", \"Contribution of mismatch discrimination in vivo not quantified\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"How LIG1 handles ribonucleotide-containing nicks during ribonucleotide excision repair was unknown; structural and biochemical studies established that LIG1 efficiently seals 3′-ribonucleotide nicks (Asp570/Arg871 contact the 2′-OH) but discriminates against 5′-ribonucleotide nicks via conformational rearrangements at Arg871, defining an asymmetric sugar-selectivity mechanism.\",\n      \"evidence\": \"X-ray crystallography of LIG1 with 3′- and 5′-RNA-DNA hybrid nick substrates, in vitro nick-sealing assays with active-site mutants\",\n      \"pmids\": [\"38522520\", \"39159820\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of asymmetric sugar discrimination for genome stability not tested\", \"Whether LIG3α shares this asymmetry not determined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"The specific active-site determinants of LIG1 mismatch fidelity were undefined; mutagenesis and structures of F635A and F872A mutants demonstrated these residues enforce DNA end rigidity and 5′-end alignment at the nick, creating a barrier to adenylate transfer on all 12 non-canonical mismatches.\",\n      \"evidence\": \"X-ray crystallography of LIG1 F635/F872 mutants with mismatched nick DNA, comprehensive biochemical ligation panel\",\n      \"pmids\": [\"39574773\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Preprint at time of discovery; awaits formal peer review\", \"Whether these residues also govern discrimination against damaged bases not fully explored\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"How LIG1 locates nick sites along DNA was unknown; single-molecule imaging revealed that the N-terminal non-catalytic domain enables one-dimensional diffusion along DNA before forming long-lived complexes at nicks, whereas the catalytic core alone binds non-specifically and transiently.\",\n      \"evidence\": \"Single-molecule TIRF and C-Trap fluorescence microscopy with full-length versus C-terminal truncation constructs\",\n      \"pmids\": [\"39404052\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether PCNA or other replication factors modulate 1D diffusion not tested\", \"In vivo diffusion parameters not measured\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"How LIG1 handles oxidative lesions inserted by pol β during BER was structurally unresolved; crystal structures captured LIG1 at pre- and post-catalytic steps with 3′-8-oxodG/8-oxorG nicks, revealing that Hoogsteen versus Watson-Crick pairing of 8-oxoG determines mutagenic or non-mutagenic ligation outcomes, and that APE1 can excise oxidatively damaged ends to limit mutagenic sealing.\",\n      \"evidence\": \"X-ray crystallography of LIG1 with 8-oxoG-containing nick substrates, in vitro ligation assays\",\n      \"pmids\": [\"38766188\", \"41370201\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular frequency of mutagenic versus non-mutagenic ligation of 8-oxoG nicks not quantified\", \"Contribution of LIG3α to 8-oxoG nick ligation in BER not compared\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether LIG1 is a therapeutic vulnerability in homologous recombination-deficient cancers was untested; multiple orthogonal depletion strategies demonstrated that LIG1 loss causes selective lethality in BRCA1-mutant cells through accumulation of single-strand breaks and replication stress, establishing LIG1 as a synthetic lethal target.\",\n      \"evidence\": \"CRISPR screens, CRISPRi, RNAi, targeted protein degradation, catalytic-dead rescue (K568A), PAR staining, xenograft models\",\n      \"pmids\": [\"39868490\", \"39718835\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether LIG1 inhibition synergizes with PARP inhibitors in clinical contexts not established\", \"Mechanism of synthetic lethality beyond nick accumulation not fully dissected\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The functional impact of the Huntington's disease-associated LIG1 K845N variant was unknown; structural, kinetic, and in vivo studies showed K845N reduces nick affinity and enhances mismatch discrimination, conferring protection against oxidative stress in cells and suppressing somatic CAG repeat expansion in HD knock-in mice.\",\n      \"evidence\": \"X-ray crystallography, pre-steady-state kinetics, TIRF single-molecule microscopy, cell-based oxidative stress assays, HD knock-in mouse model\",\n      \"pmids\": [\"41346861\", \"41770933\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether K845N affects replicative ligation efficiency in vivo not fully addressed\", \"Mechanism by which enhanced fidelity suppresses repeat expansion at the molecular level not fully defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: the structural basis of the APE1-LIG1 physical interaction; how post-translational modifications (beyond K126 methylation) regulate LIG1 activity and recruitment in vivo; and whether LIG1's 1D diffusion mechanism operates in the chromatin context and is modulated by replication/repair factors.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of an APE1-LIG1 complex\", \"In vivo regulation of LIG1 by PTMs beyond K126me largely unexplored\", \"Chromatin-context single-molecule studies of LIG1 not performed\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [0, 1, 2, 4, 5, 7, 9, 10, 11, 12]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 1, 4, 5, 6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 13]},\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [0, 15]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [1, 2, 4, 5, 8, 9, 10, 11, 12]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [2, 10, 11, 13]}\n    ],\n    \"complexes\": [\n      \"PCNA-FEN1-LIG1 toolbelt\"\n    ],\n    \"partners\": [\n      \"PCNA\",\n      \"FEN1\",\n      \"APE1\",\n      \"UHRF1\",\n      \"POLB\",\n      \"SRSF1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}