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UniProtKB/Swiss-Prot entry P04819


[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name DNLI_YEAST
Primary accession number P04819
Secondary accession number Q12736
Integrated into Swiss-Prot on August 13, 1987
Sequence was last modified on November 1, 1997 (Sequence version 2)
Annotations were last modified on    September 23, 2008 (Entry version 97)
Name and origin of the protein
Protein name DNA ligase 1 [Precursor]
Synonyms EC 6.5.1.1
DNA ligase I
Polydeoxyribonucleotide synthase [ATP] 1
Gene name
Name: CDC9
OrderedLocusNames: YDL164C
From
Saccharomyces cerevisiae (Baker's yeast) [TaxID: 4932] 
Taxonomy Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
Protein existence 1: Evidence at protein level;
References
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
DOI=10.1093/nar/13.23.8323; PubMed=3909103 [NCBI, ExPASy, EBI, Israel, Japan]
Barker D.G., White J.H.M., Johnston L.H.;
"The nucleotide sequence of the DNA ligase gene (CDC9) from Saccharomyces cerevisiae: a gene which is cell-cycle regulated and induced in response to DNA damage.";
Nucleic Acids Res. 13:8323-8337(1985).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169867 [NCBI, ExPASy, EBI, Israel, Japan]
Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
Nature 387:75-78(1997).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
DOI=10.1101/gr.6037607; PubMed=17322287 [NCBI, ExPASy, EBI, Israel, Japan]
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 610-755.
STRAIN=ATCC 38626 / AH22 / NRRL Y-12843;
PubMed=8483449 [NCBI, ExPASy, EBI, Israel, Japan]
Wehner E.P., Rao E., Brendel M.;
"Molecular structure and genetic regulation of SFA, a gene responsible for resistance to formaldehyde in Saccharomyces cerevisiae, and characterization of its protein product.";
Mol. Gen. Genet. 237:351-358(1993).
[5]
ALTERNATIVE INITIATION.
DOI=10.1016/S0960-9822(99)80477-1; PubMed=10531002 [NCBI, ExPASy, EBI, Israel, Japan]
Willer M., Rainey M., Pullen T., Stirling C.J.;
"The yeast CDC9 gene encodes both a nuclear and a mitochondrial form of DNA ligase I.";
Curr. Biol. 9:1085-1094(1999).
[6]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
DOI=10.1038/nature02046; PubMed=14562106 [NCBI, ExPASy, EBI, Israel, Japan]
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, AND MASS SPECTROMETRY.
DOI=10.1073/pnas.0607084104; PubMed=17287358 [NCBI, ExPASy, EBI, Israel, Japan]
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58, AND MASS SPECTROMETRY.
DOI=10.1073/pnas.0701622104; PubMed=17563356 [NCBI, ExPASy, EBI, Israel, Japan]
Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H.;
"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases.";
Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-58 AND SER-75, AND MASS SPECTROMETRY.
DOI=10.1074/mcp.M700468-MCP200; PubMed=18407956 [NCBI, ExPASy, EBI, Israel, Japan]
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
Comments
  • FUNCTION: This protein seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. The mitochondrial form is required for mitochondrial DNA maintenance but is non-essential while the nuclear form is essential for cell viability.
  • CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
  • INTERACTION:
    P15891:ABP1; NbExp=1; IntAct=EBI-5991, EBI-2036;
  • SUBCELLULAR LOCATION: Nucleus. Mitochondrion.
  • ALTERNATIVE PRODUCTS: 2 named isoforms [FASTA] produced by alternative initiation.
    NameMitochondrial
    Isoform IDP04819-1
    This is the isoform sequence displayed in this entry.
    NameNuclear
    Isoform IDP04819-2
    Features which should be applied to build the isoform sequence: VSP_018719.
  • MISCELLANEOUS: Cdc9 is included within the category of so-called 'start genes', encoding proteins which are required in early G1, when the cell is faced with the option of initiating a further cell cycle.
  • MISCELLANEOUS: Present with 149 molecules/cell in log phase SD medium.
  • SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
X03246; CAA27005.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
Z67750; CAA91582.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
Z74212; CAA98737.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
AY723764; AAU09681.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
X68020; CAA48158.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR S61049; LQBYPX.
RefSeq NP_010117.1; -.
3D structure databases
ModBase P04819.
Protein-protein interaction databases
DIP DIP:5630N; -.
IntAct P04819; -.
Organism-specific databases
CYGD YDL164c; -.
SGD S000002323; CDC9.
Yeast-GFP YDL164C.
Gene expression databases
ArrayExpress P04819; -.
GermOnline YDL164C; Saccharomyces cerevisiae.
Ontologies
GO
GO:0005739; Cellular component: mitochondrion (inferred from direct assay from SGD).
GO:0005634; Cellular component: nucleus (inferred from direct assay from SGD).
GO:0005657; Cellular component: replication fork (non-traceable author statement from SGD).
GO:0003910; Molecular function: DNA ligase (ATP) activity (inferred from direct assay from SGD).
GO:0005515; Molecular function: protein binding (inferred from physical interaction from IntAct).
GO:0006284; Biological process: base-excision repair (inferred from mutant phenotype from SGD).
GO:0006266; Biological process: DNA ligation (inferred from direct assay from SGD).
GO:0006310; Biological process: DNA recombination (inferred from mutant phenotype from SGD).
GO:0006273; Biological process: lagging strand elongation (inferred from direct assay from SGD).
GO:0000278; Biological process: mitotic cell cycle (inferred from mutant phenotype from SGD).
GO:0006289; Biological process: nucleotide-excision repair (inferred from mutant phenotype from SGD).
QuickGo view.
Family and domain databases
InterPro IPR000977; DNA_ligase.
IPR012309; DNA_ligase_A_C.
IPR012310; DNA_ligase_A_M.
IPR012308; DNA_ligase_A_N.
IPR016059; DNA_ligase_CS.
IPR012340; NA-bd_OB-fold.
Graphical view of domain structure.
Gene3D G3DSA:2.40.50.140; OB_NA_bd_sub; 1.
Pfam PF04679; DNA_ligase_A_C; 1.
PF01068; DNA_ligase_A_M; 1.
PF04675; DNA_ligase_A_N; 1.
Pfam graphical view of domain structure.
TIGRFAMs TIGR00574; dnl1; 1.
PROSITE PS00697; DNA_LIGASE_A1; 1.
PS00333; DNA_LIGASE_A2; 1.
PS50160; DNA_LIGASE_A3; 1.
PROSITE graphical view of domain structure (profiles).
BLOCKS P04819.
Proteomic databases
PeptideAtlas P04819; -.
Genome annotation databases
Ensembl YDL164C; Saccharomyces cerevisiae. [Contig view]
GeneID 851391; -.
GenomeReviews Z71256_GR; YDL164C.
KEGG sce:YDL164C; -.
NMPDR fig|4932.3.peg.851; -.
Phylogenomic databases
HOGENOM P04819; -.
Other
LinkHub P04819; -.
ProtoNet P04819.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
Alternative initiation; ATP-binding; Cell cycle; Cell division; Complete proteome; DNA damage; DNA recombination; DNA repair; DNA replication; Ligase; Mitochondrion; Nucleotide-binding; Nucleus; Phosphoprotein; Transit peptide.
Features
SEVIEWER logo Feature table viewer
KeyFrom   To Length Description FTId
TRANSIT   1    44  44     Mitochondrion (Potential). 
CHAIN   45   755  711     DNA ligase 1. PRO_0000007274
ACT_SITE   419   419        N6-AMP-lysine intermediate (By similarity). 
MOD_RES   58    58        Phosphoserine. 
MOD_RES   75    75        Phosphoserine. 
VAR_SEQ   1    23        Missing (in isoform Nuclear). VSP_018719
CONFLICT   69    69        D -> E (in Ref. 1; CAA27005). 
CONFLICT   186   186        L -> V (in Ref. 1; CAA27005). 
CONFLICT   671   671        G -> E (in Ref. 4; CAA48158). 
CONFLICT   724   724        R -> I (in Ref. 4; CAA48158). 
Sequence information
Length: 755 AA [This is the length of the unprocessed precursor] Molecular weight: 84828 Da [This is the MW of the unprocessed precursor] CRC64: B7C2ECAF5C61CAE7 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MRRLLTGCLL SSARPLKSRL PLLMSSSLPS SAGKKPKQAT LARFFTSMKN KPTEGTPSPK 

        70         80         90        100        110        120 
KSSKHMLEDR MDNVSGEEEY ATKKLKQTAV THTVAAPSSM GSNFSSIPSS APSSGVADSP 

       130        140        150        160        170        180 
QQSQRLVGEV EDALSSNNND HYSSNIPYSE VCEVFNKIEA ISSRLEIIRI CSDFFIKIMK 

       190        200        210        220        230        240 
QSSKNLIPTT YLFINRLGPD YEAGLELGLG ENLLMKTISE TCGKSMSQIK LKYKDIGDLG 

       250        260        270        280        290        300 
EIAMGARNVQ PTMFKPKPLT VGEVFKNLRA IAKTQGKDSQ LKKMKLIKRM LTACKGIEAK 

       310        320        330        340        350        360 
FLIRSLESKL RIGLAEKTVL ISLSKALLLH DENREDSPDK DVPMDVLESA QQKIRDAFCQ 

       370        380        390        400        410        420 
VPNYEIVINS CLEHGIMNLD KYCTLRPGIP LKPMLAKPTK AINEVLDRFQ GETFTSEYKY 

       430        440        450        460        470        480 
DGERAQVHLL NDGTMRIYSR NGENMTERYP EINITDFIQD LDTTKNLILD CEAVAWDKDQ 

       490        500        510        520        530        540 
GKILPFQVLS TRKRKDVELN DVKVKVCLFA FDILCYNDER LINKSLKERR EYLTKVTKVV 

       550        560        570        580        590        600 
PGEFQYATQI TTNNLDELQK FLDESVNHSC EGLMVKMLEG PESHYEPSKR SRNWLKLKKD 

       610        620        630        640        650        660 
YLEGVGDSLD LCVLGAYYGR GKRTGTYGGF LLGCYNQDTG EFETCCKIGT GFSDEMLQLL 

       670        680        690        700        710        720 
HDRLTPTIID GPKATFVFDS SAEPDVWFEP TTLFEVLTAD LSLSPIYKAG SATFDKGVSL 

       730        740        750 
RFPRFLRIRE DKGVEDATSS DQIVELYENQ SHMQN 

P04819 in FASTA format

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