ID DNLI1_YEAST Reviewed; 755 AA. AC P04819; D6VRI7; Q12736; DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot. DT 01-NOV-1997, sequence version 2. DT 27-MAR-2024, entry version 229. DE RecName: Full=DNA ligase 1; DE EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135}; DE AltName: Full=DNA ligase I; DE AltName: Full=Polydeoxyribonucleotide synthase [ATP] 1; DE Flags: Precursor; GN Name=CDC9; OrderedLocusNames=YDL164C; OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast). OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; OC Saccharomycetales; Saccharomycetaceae; Saccharomyces. OX NCBI_TaxID=559292; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=3909103; DOI=10.1093/nar/13.23.8323; RA Barker D.G., White J.H.M., Johnston L.H.; RT "The nucleotide sequence of the DNA ligase gene (CDC9) from Saccharomyces RT cerevisiae: a gene which is cell-cycle regulated and induced in response to RT DNA damage."; RL Nucleic Acids Res. 13:8323-8337(1985). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=9169867; RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., RA Mewes H.-W., Zollner A., Zaccaria P.; RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."; RL Nature 387:75-78(1997). RN [3] RP GENOME REANNOTATION. RC STRAIN=ATCC 204508 / S288c; RX PubMed=24374639; DOI=10.1534/g3.113.008995; RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.; RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now."; RL G3 (Bethesda) 4:389-398(2014). RN [4] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=17322287; DOI=10.1101/gr.6037607; RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J., RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., RA LaBaer J.; RT "Approaching a complete repository of sequence-verified protein-encoding RT clones for Saccharomyces cerevisiae."; RL Genome Res. 17:536-543(2007). RN [5] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 610-755. RC STRAIN=ATCC 38626 / AH22 / NRRL Y-12843; RX PubMed=8483449; DOI=10.1007/bf00279438; RA Wehner E.P., Rao E., Brendel M.; RT "Molecular structure and genetic regulation of SFA, a gene responsible for RT resistance to formaldehyde in Saccharomyces cerevisiae, and RT characterization of its protein product."; RL Mol. Gen. Genet. 237:351-358(1993). RN [6] RP ALTERNATIVE INITIATION. RX PubMed=10531002; DOI=10.1016/s0960-9822(99)80477-1; RA Willer M., Rainey M., Pullen T., Stirling C.J.; RT "The yeast CDC9 gene encodes both a nuclear and a mitochondrial form of DNA RT ligase I."; RL Curr. Biol. 9:1085-1094(1999). RN [7] RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS]. RX PubMed=14562106; DOI=10.1038/nature02046; RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., RA O'Shea E.K., Weissman J.S.; RT "Global analysis of protein expression in yeast."; RL Nature 425:737-741(2003). RN [8] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=17287358; DOI=10.1073/pnas.0607084104; RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.; RT "Analysis of phosphorylation sites on proteins from Saccharomyces RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry."; RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007). RN [9] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200; RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.; RT "A multidimensional chromatography technology for in-depth phosphoproteome RT analysis."; RL Mol. Cell. Proteomics 7:1389-1396(2008). RN [10] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-75; SER-119 AND SER-123, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=19779198; DOI=10.1126/science.1172867; RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.; RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights RT into evolution."; RL Science 325:1682-1686(2009). RN [11] RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2 (ISOFORM NUCLEAR), CLEAVAGE OF RP INITIATOR METHIONINE [LARGE SCALE ANALYSIS] (ISOFORM NUCLEAR), AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=22814378; DOI=10.1073/pnas.1210303109; RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.; RT "N-terminal acetylome analyses and functional insights of the N-terminal RT acetyltransferase NatB."; RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012). CC -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA CC replication, DNA recombination and DNA repair. The mitochondrial form CC is required for mitochondrial DNA maintenance but is non-essential CC while the nuclear form is essential for cell viability. CC -!- CATALYTIC ACTIVITY: CC Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + CC diphosphate.; EC=6.5.1.1; Evidence={ECO:0000255|PROSITE- CC ProRule:PRU10135}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250}; CC -!- SUBCELLULAR LOCATION: [Isoform Mitochondrial]: Mitochondrion. CC -!- SUBCELLULAR LOCATION: [Isoform Nuclear]: Nucleus. CC -!- ALTERNATIVE PRODUCTS: CC Event=Alternative initiation; Named isoforms=2; CC Name=Mitochondrial; CC IsoId=P04819-1; Sequence=Displayed; CC Name=Nuclear; CC IsoId=P04819-2; Sequence=VSP_018719; CC -!- MISCELLANEOUS: Cdc9 is included within the category of so-called 'start CC genes', encoding proteins which are required in early G1, when the cell CC is faced with the option of initiating a further cell cycle. CC -!- MISCELLANEOUS: Present with 149 molecules/cell in log phase SD medium. CC {ECO:0000269|PubMed:14562106}. CC -!- MISCELLANEOUS: [Isoform Nuclear]: Produced by alternative initiation at CC Met-24 of isoform Mitochondrial. {ECO:0000305}. CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family. CC {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X03246; CAA27005.1; -; Genomic_DNA. DR EMBL; Z67750; CAA91582.1; -; Genomic_DNA. DR EMBL; Z74212; CAA98737.1; -; Genomic_DNA. DR EMBL; AY723764; AAU09681.1; -; Genomic_DNA. DR EMBL; X68020; CAA48158.1; -; Genomic_DNA. DR EMBL; BK006938; DAA11697.1; -; Genomic_DNA. DR PIR; S61049; LQBYPX. DR RefSeq; NP_010117.1; NM_001180224.1. [P04819-1] DR PDB; 2OD8; X-ray; 2.80 A; B=32-53. DR PDBsum; 2OD8; -. DR AlphaFoldDB; P04819; -. DR SMR; P04819; -. DR BioGRID; 31901; 483. DR DIP; DIP-5630N; -. DR ELM; P04819; -. DR IntAct; P04819; 37. DR MINT; P04819; -. DR STRING; 4932.YDL164C; -. DR iPTMnet; P04819; -. DR MaxQB; P04819; -. DR PaxDb; 4932-YDL164C; -. DR PeptideAtlas; P04819; -. DR EnsemblFungi; YDL164C_mRNA; YDL164C; YDL164C. [P04819-1] DR GeneID; 851391; -. DR KEGG; sce:YDL164C; -. DR AGR; SGD:S000002323; -. DR SGD; S000002323; CDC9. DR VEuPathDB; FungiDB:YDL164C; -. DR eggNOG; KOG0967; Eukaryota. DR GeneTree; ENSGT00940000157783; -. DR HOGENOM; CLU_005138_4_1_1; -. DR InParanoid; P04819; -. DR OMA; WIKYKRD; -. DR OrthoDB; 961at2759; -. DR BioCyc; YEAST:G3O-29556-MONOMER; -. DR Reactome; R-SCE-5358565; Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha). DR Reactome; R-SCE-5358606; Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta). DR Reactome; R-SCE-69183; Processive synthesis on the lagging strand. DR BioGRID-ORCS; 851391; 6 hits in 10 CRISPR screens. DR EvolutionaryTrace; P04819; -. DR PRO; PR:P04819; -. DR Proteomes; UP000002311; Chromosome IV. DR RNAct; P04819; Protein. DR GO; GO:0005739; C:mitochondrion; IDA:SGD. DR GO; GO:0005634; C:nucleus; IDA:SGD. DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW. DR GO; GO:0003677; F:DNA binding; IEA:InterPro. DR GO; GO:0003910; F:DNA ligase (ATP) activity; IDA:SGD. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0006284; P:base-excision repair; IMP:SGD. DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW. DR GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro. DR GO; GO:0006266; P:DNA ligation; IDA:SGD. DR GO; GO:0006310; P:DNA recombination; IMP:SGD. DR GO; GO:0006273; P:lagging strand elongation; IDA:SGD. DR GO; GO:0035753; P:maintenance of DNA trinucleotide repeats; IMP:SGD. DR GO; GO:0000278; P:mitotic cell cycle; IMP:SGD. DR GO; GO:0006289; P:nucleotide-excision repair; IMP:SGD. DR GO; GO:1903461; P:Okazaki fragment processing involved in mitotic DNA replication; IBA:GO_Central. DR CDD; cd07900; Adenylation_DNA_ligase_I_Euk; 1. DR CDD; cd07969; OBF_DNA_ligase_I; 1. DR Gene3D; 3.30.1490.70; -; 1. DR Gene3D; 1.10.3260.10; DNA ligase, ATP-dependent, N-terminal domain; 1. DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1. DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1. DR IDEAL; IID50307; -. DR InterPro; IPR000977; DNA_ligase_ATP-dep. DR InterPro; IPR012309; DNA_ligase_ATP-dep_C. DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent. DR InterPro; IPR016059; DNA_ligase_ATP-dep_CS. DR InterPro; IPR012308; DNA_ligase_ATP-dep_N. DR InterPro; IPR036599; DNA_ligase_N_sf. DR InterPro; IPR012340; NA-bd_OB-fold. DR NCBIfam; TIGR00574; dnl1; 1. DR PANTHER; PTHR45674:SF4; DNA LIGASE 1; 1. DR PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 1. DR Pfam; PF04679; DNA_ligase_A_C; 1. DR Pfam; PF01068; DNA_ligase_A_M; 1. DR Pfam; PF04675; DNA_ligase_A_N; 1. DR SUPFAM; SSF117018; ATP-dependent DNA ligase DNA-binding domain; 1. DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1. DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1. DR PROSITE; PS00697; DNA_LIGASE_A1; 1. DR PROSITE; PS00333; DNA_LIGASE_A2; 1. DR PROSITE; PS50160; DNA_LIGASE_A3; 1. PE 1: Evidence at protein level; KW 3D-structure; Acetylation; Alternative initiation; ATP-binding; Cell cycle; KW Cell division; DNA damage; DNA recombination; DNA repair; DNA replication; KW Ligase; Magnesium; Metal-binding; Mitochondrion; Nucleotide-binding; KW Nucleus; Phosphoprotein; Reference proteome; Transit peptide. FT TRANSIT 1..44 FT /note="Mitochondrion" FT /evidence="ECO:0000255" FT CHAIN 45..755 FT /note="DNA ligase 1" FT /id="PRO_0000007274" FT REGION 47..79 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 97..127 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 309..318 FT /note="Interaction with target DNA" FT /evidence="ECO:0000250" FT REGION 493..495 FT /note="Interaction with target DNA" FT /evidence="ECO:0000250" FT COMPBIAS 61..79 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 419 FT /note="N6-AMP-lysine intermediate" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10135" FT BINDING 417 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT BINDING 424 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT BINDING 440 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT BINDING 472 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000250" FT BINDING 571 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000250" FT BINDING 576 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT BINDING 590 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT BINDING 596 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT SITE 164 FT /note="Interaction with target DNA" FT /evidence="ECO:0000250" FT SITE 441 FT /note="Interaction with target DNA" FT /evidence="ECO:0000250" FT SITE 622 FT /note="Interaction with target DNA" FT /evidence="ECO:0000250" FT SITE 647 FT /note="Interaction with target DNA" FT /evidence="ECO:0000250" FT MOD_RES 58 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:17287358, FT ECO:0007744|PubMed:18407956" FT MOD_RES 75 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:17287358, FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198" FT MOD_RES 119 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:19779198" FT MOD_RES 123 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:19779198" FT VAR_SEQ 1..23 FT /note="Missing (in isoform Nuclear)" FT /evidence="ECO:0000305" FT /id="VSP_018719" FT CONFLICT 69 FT /note="D -> E (in Ref. 1; CAA27005)" FT /evidence="ECO:0000305" FT CONFLICT 186 FT /note="L -> V (in Ref. 1; CAA27005)" FT /evidence="ECO:0000305" FT CONFLICT 671 FT /note="G -> E (in Ref. 5; CAA48158)" FT /evidence="ECO:0000305" FT CONFLICT 724 FT /note="R -> I (in Ref. 5; CAA48158)" FT /evidence="ECO:0000305" FT HELIX 41..44 FT /evidence="ECO:0007829|PDB:2OD8" FT INIT_MET P04819-2:1 FT /note="Removed" FT /evidence="ECO:0007744|PubMed:22814378" FT MOD_RES P04819-2:2 FT /note="N-acetylserine" FT /evidence="ECO:0007744|PubMed:22814378" SQ SEQUENCE 755 AA; 84828 MW; B7C2ECAF5C61CAE7 CRC64; MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN KPTEGTPSPK KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM GSNFSSIPSS APSSGVADSP QQSQRLVGEV EDALSSNNND HYSSNIPYSE VCEVFNKIEA ISSRLEIIRI CSDFFIKIMK QSSKNLIPTT YLFINRLGPD YEAGLELGLG ENLLMKTISE TCGKSMSQIK LKYKDIGDLG EIAMGARNVQ PTMFKPKPLT VGEVFKNLRA IAKTQGKDSQ LKKMKLIKRM LTACKGIEAK FLIRSLESKL RIGLAEKTVL ISLSKALLLH DENREDSPDK DVPMDVLESA QQKIRDAFCQ VPNYEIVINS CLEHGIMNLD KYCTLRPGIP LKPMLAKPTK AINEVLDRFQ GETFTSEYKY DGERAQVHLL NDGTMRIYSR NGENMTERYP EINITDFIQD LDTTKNLILD CEAVAWDKDQ GKILPFQVLS TRKRKDVELN DVKVKVCLFA FDILCYNDER LINKSLKERR EYLTKVTKVV PGEFQYATQI TTNNLDELQK FLDESVNHSC EGLMVKMLEG PESHYEPSKR SRNWLKLKKD YLEGVGDSLD LCVLGAYYGR GKRTGTYGGF LLGCYNQDTG EFETCCKIGT GFSDEMLQLL HDRLTPTIID GPKATFVFDS SAEPDVWFEP TTLFEVLTAD LSLSPIYKAG SATFDKGVSL RFPRFLRIRE DKGVEDATSS DQIVELYENQ SHMQN //