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UniProtKB/Swiss-Prot entry Q08387


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

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Entry information
Entry name DNL4_YEAST
Primary accession number Q08387
Secondary accession numbers Q02913 Q02914
Integrated into Swiss-Prot on November 1, 1997
Sequence was last modified on November 1, 1996 (Sequence version 1)
Annotations were last modified on    September 2, 2008 (Entry version 68)
Name and origin of the protein
Protein name DNA ligase 4
Synonyms EC 6.5.1.1
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
DNA ligase II
Gene name
Name: DNL4
Synonyms: LIG4
OrderedLocusNames: YOR005C
ORFNames: UND407, UNE452
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=10.1002/(SICI)1097-0061(199609)12:10B<1091::AID-YEA22>3.3.CO;2-9; PubMed=8896276 [NCBI, ExPASy, EBI, Israel, Japan]
Sterky F., Holmberg A., Pettersson B., Uhlen M.;
"The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes.";
Yeast 12:1091-1095(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=9169874 [NCBI, ExPASy, EBI, Israel, Japan]
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
Nature 387:98-102(1997).
[3]
CHARACTERIZATION.
DOI=10.1093/nar/25.8.1485; PubMed=9092653 [NCBI, ExPASy, EBI, Israel, Japan]
Ramos W., Tappe N., Talamantez J., Friedberg E.C., Tomkinson A.E.;
"Two distinct DNA ligase activities in mitotic extracts of the yeast Saccharomyces cerevisiae.";
Nucleic Acids Res. 25:1485-1492(1997).
[4]
INTERACTION WITH LIF1.
DOI=10.1093/emboj/17.14.4188; PubMed=9670033 [NCBI, ExPASy, EBI, Israel, Japan]
Herrmann G., Lindahl T., Schar P.;
"Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand break repair related to mammalian XRCC4.";
EMBO J. 17:4188-4198(1998).
[5]
INTERACTION WITH POL4.
DOI=10.1074/jbc.M206861200; PubMed=12235149 [NCBI, ExPASy, EBI, Israel, Japan]
Tseng H.-M., Tomkinson A.E.;
"A physical and functional interaction between yeast Pol4 and Dnl4-Lif1 links DNA synthesis and ligation in nonhomologous end joining.";
J. Biol. Chem. 277:45630-45637(2002).
[6]
X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 681-944 IN COMPLEX WITH LIF1.
DOI=10.1016/j.dnarep.2005.11.004; PubMed=16388993 [NCBI, ExPASy, EBI, Israel, Japan]
Dore A.S., Furnham N., Davies O.R., Sibanda B.L., Chirgadze D.Y., Jackson S.P., Pellegrini L., Blundell T.L.;
"Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode.";
DNA Repair 5:362-368(2006).
Comments
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
U43491; AAC49485.1; ALT_FRAME; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
U43491; AAC49484.1; ALT_FRAME; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
Z74913; CAA99193.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR S66870; S66870.
RefSeq NP_014647.1; -.
3D structure databases
PDB
1Z56; X-ray; 3.92 A; C=681-944.[ExPASy / RCSB / EBI]
PDBsum 1Z56; -.
ModBase Q08387.
Protein-protein interaction databases
DIP DIP:5801N; -.
IntAct Q08387; -.
Organism-specific databases
CYGD YOR005c; -.
SGD S000005531; DNL4.
Yeast-GFP YOR005C.
Gene expression databases
ArrayExpress Q08387; -.
GermOnline YOR005C; Saccharomyces cerevisiae.
Ontologies
GO
GO:0032807; Cellular component: DNA ligase IV complex (inferred from physical interaction from SGD).
GO:0003910; Molecular function: DNA ligase (ATP) activity (inferred from direct assay from SGD).
GO:0006303; Biological process: double-strand break repair via nonhomologous end joining (inferred from direct assay from SGD).
GO:0001302; Biological process: replicative cell aging (inferred from genetic interaction from SGD).
QuickGo view.
Family and domain databases
InterPro IPR001357; BRCT.
IPR000977; DNA_ligase.
IPR012310; DNA_ligase_A_M.
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 PF00533; BRCT; 2.
PF01068; DNA_ligase_A_M; 1.
Pfam graphical view of domain structure.
SMART SM00292; BRCT; 1.
SMART graphical view of domain structure.
TIGRFAMs TIGR00574; dnl1; 1.
PROSITE PS50172; BRCT; 2.
PS00697; DNA_LIGASE_A1; 1.
PS00333; DNA_LIGASE_A2; 1.
PS50160; DNA_LIGASE_A3; 1.
PROSITE graphical view of domain structure (profiles).
BLOCKS Q08387.
Genome annotation databases
Ensembl YOR005C; Saccharomyces cerevisiae. [Contig view]
GeneID 854166; -.
GenomeReviews Y13140_GR; YOR005C.
KEGG sce:YOR005C; -.
NMPDR fig|4932.3.peg.5742; -.
Phylogenomic databases
HOGENOM Q08387; -.
Other
LinkHub Q08387; -.
ProtoNet Q08387.
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; ATP-binding; Cell cycle; Cell division; Complete proteome; DNA damage; DNA recombination; DNA repair; DNA replication; Ligase; Nucleotide-binding; Nucleus; Repeat.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
CHAIN   1   944  944     DNA ligase 4. PRO_0000059582
DOMAIN   681   780  100     BRCT 1. 
DOMAIN   836   941  106     BRCT 2. 
ACT_SITE   282   282        N6-AMP-lysine intermediate (By similarity). 
STRAND   694   698  5      
STRAND   704   707  4      
HELIX   712   719  8      
STRAND   737   740  4      
HELIX   745   750  6      
TURN   751   754  4      
HELIX   764   767  4      
TURN   784   787  4      
HELIX   788   791  4      
HELIX   792   794  3      
STRAND   797   799  3      
STRAND   801   804  4      
HELIX   808   813  6      
HELIX   861   867  7      
STRAND   875   877  3      
STRAND   879   882  4      
TURN   888   890  3      
HELIX   891   894  4      
HELIX   897   900  4      
TURN   901   907  7      
STRAND   908   911  4      
STRAND   917   919  3      
HELIX   922   928  7      
Sequence information
Length: 944 AA [This is the length of the unprocessed precursor] Molecular weight: 108515 Da [This is the MW of the unprocessed precursor] CRC64: 7FB6D7927E1719B5 [This is a checksum on the sequence]
        10         20         30         40         50         60 
MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY YEIISNFVEM 

        70         80         90        100        110        120 
WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL KLPKNSATEQ RLKDWKQRVG 

       130        140        150        160        170        180 
KGGNLSSLLV EEIAKRRAEP SSKAITIDNV NHYLDSLSGD RFASGRGFKS LVKSKPFLHC 

       190        200        210        220        230        240 
VENMSFVELK YFFDIVLKNR VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR 

       250        260        270        280        290        300 
LKDDDLSIKV GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK 

       310        320        330        340        350        360 
FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV ILPFGLVKGS 

       370        380        390        400        410        420 
AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR KQYLNSILSP LKNIVEIVRS 

       430        440        450        460        470        480 
SRCYGVESIK KSLEVAISLG SEGVVLKYYN SSYNVASRNN NWIKVKPEYL EEFGENLDLI 

       490        500        510        520        530        540 
VIGRDSGKKD SFMLGLLVLD EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI 

       550        560        570        580        590        600 
ANGISQEEFK EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD 

       610        620        630        640        650        660 
NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY QAERSQLGLI 

       670        680        690        700        710        720 
RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE DTGIRITRAE LEKTIVEHGG 

       730        740        750        760        770        780 
KLIYNVILKR HSIGDVRLIS CKTTTECKAL IDRGYDILHP NWVLDCIAYK RLILIEPNYC 

       790        800        810        820        830        840 
FNVSQKMRAV AEKRVDCLGD SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL 

       850        860        870        880        890        900 
FSNRIAYVPR RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE 

       910        920        930        940 
KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY 

Q08387 in FASTA format

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