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Database: UniProt
Entry: Q08387
LinkDB: Q08387
Original site: Q08387 
ID   DNLI4_YEAST             Reviewed;         944 AA.
AC   Q08387; D6W271; Q02913; Q02914;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   22-NOV-2017, entry version 158.
DE   RecName: Full=DNA ligase 4;
DE            EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135};
DE   AltName: Full=DNA ligase II;
DE   AltName: Full=DNA ligase IV;
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] 4;
GN   Name=DNL4; Synonyms=LIG4; OrderedLocusNames=YOR005C;
GN   ORFNames=UND407, UNE452;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
OC   Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=8896276;
RX   DOI=10.1002/(SICI)1097-0061(199609)12:10B<1091::AID-YEA22>3.3.CO;2-9;
RA   Sterky F., Holmberg A., Pettersson B., Uhlen M.;
RT   "The sequence of a 30 kb fragment on the left arm of chromosome XV
RT   from Saccharomyces cerevisiae reveals 15 open reading frames, five of
RT   which correspond to previously identified genes.";
RL   Yeast 12:1091-1095(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169874;
RA   Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
RA   Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
RA   Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
RA   Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
RA   Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
RA   Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
RA   Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
RA   Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
RA   Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
RA   Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
RA   Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
RA   Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
RA   Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
RA   Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
RA   Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
RA   Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
RA   Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
RA   Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
RA   Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
RL   Nature 387:98-102(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.,
RA   Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and
RT   now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   CHARACTERIZATION.
RX   PubMed=9092653; DOI=10.1093/nar/25.8.1485;
RA   Ramos W., Tappe N., Talamantez J., Friedberg E.C., Tomkinson A.E.;
RT   "Two distinct DNA ligase activities in mitotic extracts of the yeast
RT   Saccharomyces cerevisiae.";
RL   Nucleic Acids Res. 25:1485-1492(1997).
RN   [5]
RP   INTERACTION WITH LIF1.
RX   PubMed=9670033; DOI=10.1093/emboj/17.14.4188;
RA   Herrmann G., Lindahl T., Schar P.;
RT   "Saccharomyces cerevisiae LIF1: a function involved in DNA double-
RT   strand break repair related to mammalian XRCC4.";
RL   EMBO J. 17:4188-4198(1998).
RN   [6]
RP   INTERACTION WITH POL4.
RX   PubMed=12235149; DOI=10.1074/jbc.M206861200;
RA   Tseng H.-M., Tomkinson A.E.;
RT   "A physical and functional interaction between yeast Pol4 and Dnl4-
RT   Lif1 links DNA synthesis and ligation in nonhomologous end joining.";
RL   J. Biol. Chem. 277:45630-45637(2002).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 681-944 IN COMPLEX WITH
RP   LIF1.
RX   PubMed=16388993; DOI=10.1016/j.dnarep.2005.11.004;
RA   Dore A.S., Furnham N., Davies O.R., Sibanda B.L., Chirgadze D.Y.,
RA   Jackson S.P., Pellegrini L., Blundell T.L.;
RT   "Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a
RT   novel BRCT interaction mode.";
RL   DNA Repair 5:362-368(2006).
CC   -!- FUNCTION: Has minor DNA joining activity. Can act on
CC       oligo(PDT)/poly(rA) substrate.
CC   -!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
CC       5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
CC       AMP + diphosphate. {ECO:0000255|PROSITE-ProRule:PRU10135}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC   -!- SUBUNIT: Interacts with LIF1 via its BRCT domain. Interacts with
CC       POL4 in the DNL4-LIF1 complex. {ECO:0000269|PubMed:12235149,
CC       ECO:0000269|PubMed:16388993, ECO:0000269|PubMed:9670033}.
CC   -!- INTERACTION:
CC       P53150:LIF1; NbExp=3; IntAct=EBI-5983, EBI-23865;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAC49484.1; Type=Frameshift; Positions=408, 413; Note=Produces 2 separate ORFs.; Evidence={ECO:0000305};
CC       Sequence=AAC49485.1; Type=Frameshift; Positions=408, 413; Note=Produces 2 separate ORFs.; Evidence={ECO:0000305};
DR   EMBL; U43491; AAC49485.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; U43491; AAC49484.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; Z74913; CAA99193.1; -; Genomic_DNA.
DR   EMBL; BK006948; DAA10787.1; -; Genomic_DNA.
DR   PIR; S66870; S66870.
DR   RefSeq; NP_014647.1; NM_001183424.1.
DR   PDB; 1Z56; X-ray; 3.92 A; C=681-943.
DR   PDBsum; 1Z56; -.
DR   ProteinModelPortal; Q08387; -.
DR   SMR; Q08387; -.
DR   BioGrid; 34408; 244.
DR   DIP; DIP-5801N; -.
DR   IntAct; Q08387; 22.
DR   MINT; MINT-672762; -.
DR   STRING; 4932.YOR005C; -.
DR   iPTMnet; Q08387; -.
DR   PRIDE; Q08387; -.
DR   EnsemblFungi; YOR005C; YOR005C; YOR005C.
DR   GeneID; 854166; -.
DR   KEGG; sce:YOR005C; -.
DR   EuPathDB; FungiDB:YOR005C; -.
DR   SGD; S000005531; DNL4.
DR   GeneTree; ENSGT00860000133881; -.
DR   HOGENOM; HOG000093622; -.
DR   InParanoid; Q08387; -.
DR   KO; K10777; -.
DR   OMA; HMCPSTK; -.
DR   OrthoDB; EOG092C18KW; -.
DR   BioCyc; YEAST:G3O-33555-MONOMER; -.
DR   BRENDA; 6.5.1.1; 984.
DR   EvolutionaryTrace; Q08387; -.
DR   PRO; PR:Q08387; -.
DR   Proteomes; UP000002311; Chromosome XV.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0032807; C:DNA ligase IV complex; IPI: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:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR   GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR   GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR   GO; GO:0051103; P:DNA ligation involved in DNA repair; IBA:GO_Central.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IDA:SGD.
DR   GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR   GO; GO:0001302; P:replicative cell aging; IGI:SGD.
DR   CDD; cd00027; BRCT; 1.
DR   Gene3D; 3.40.50.10190; -; 2.
DR   InterPro; IPR001357; BRCT_dom.
DR   InterPro; IPR036420; BRCT_dom_sf.
DR   InterPro; IPR000977; DNA_ligase_ATP-dep.
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; IPR029710; LIG4.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   PANTHER; PTHR10459:SF7; PTHR10459:SF7; 1.
DR   Pfam; PF00533; BRCT; 2.
DR   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF04675; DNA_ligase_A_N; 1.
DR   SMART; SM00292; BRCT; 1.
DR   SUPFAM; SSF50249; SSF50249; 2.
DR   SUPFAM; SSF52113; SSF52113; 3.
DR   TIGRFAMs; TIGR00574; dnl1; 1.
DR   PROSITE; PS50172; BRCT; 2.
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; ATP-binding; Cell cycle; Cell division;
KW   Complete proteome; DNA damage; DNA recombination; DNA repair;
KW   DNA replication; Ligase; Magnesium; Metal-binding; Nucleotide-binding;
KW   Nucleus; Reference proteome; Repeat.
FT   CHAIN         1    944       DNA ligase 4.
FT                                /FTId=PRO_0000059582.
FT   DOMAIN      681    780       BRCT 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00033}.
FT   DOMAIN      836    941       BRCT 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00033}.
FT   ACT_SITE    282    282       N6-AMP-lysine intermediate.
FT                                {ECO:0000255|PROSITE-ProRule:PRU10135}.
FT   METAL       340    340       Magnesium 1. {ECO:0000255}.
FT   METAL       442    442       Magnesium 2. {ECO:0000255}.
FT   BINDING     280    280       ATP. {ECO:0000250}.
FT   BINDING     287    287       ATP. {ECO:0000250}.
FT   BINDING     304    304       ATP. {ECO:0000250}.
FT   BINDING     447    447       ATP. {ECO:0000250}.
FT   BINDING     458    458       ATP. {ECO:0000250}.
FT   BINDING     464    464       ATP. {ECO:0000250}.
SQ   SEQUENCE   944 AA;  108515 MW;  7FB6D7927E1719B5 CRC64;
     MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY YEIISNFVEM
     WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL KLPKNSATEQ RLKDWKQRVG
     KGGNLSSLLV EEIAKRRAEP SSKAITIDNV NHYLDSLSGD RFASGRGFKS LVKSKPFLHC
     VENMSFVELK YFFDIVLKNR VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR
     LKDDDLSIKV GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK
     FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV ILPFGLVKGS
     AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR KQYLNSILSP LKNIVEIVRS
     SRCYGVESIK KSLEVAISLG SEGVVLKYYN SSYNVASRNN NWIKVKPEYL EEFGENLDLI
     VIGRDSGKKD SFMLGLLVLD EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI
     ANGISQEEFK EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD
     NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY QAERSQLGLI
     RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE DTGIRITRAE LEKTIVEHGG
     KLIYNVILKR HSIGDVRLIS CKTTTECKAL IDRGYDILHP NWVLDCIAYK RLILIEPNYC
     FNVSQKMRAV AEKRVDCLGD SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL
     FSNRIAYVPR RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE
     KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY
//
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