DNLI4_YEAST
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 03-AUG-2022, entry version 187.
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; Saccharomycetes;
OC 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>3.0.co;2-i;
RA Sterky F., Holmberg A., Pettersson B., Uhlen M.;
RT "The sequence of a 30 kb fragment on the left arm of chromosome XV from
RT Saccharomyces cerevisiae reveals 15 open reading frames, five of which
RT 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., Arino J.,
RA Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A.,
RA Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B.,
RA Dang V.-D., de Haan M., Delius H., Durand P., Fairhead C., Feldmann H.,
RA Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E.,
RA Grivell L.A., 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., Maarse A.C.,
RA Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G.,
RA Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B.,
RA Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F.,
RA Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E.,
RA Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I.,
RA Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H.,
RA Wiemann S., 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., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and 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-strand
RT 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-Lif1
RT 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 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 novel
RT 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:
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 -!- SUBUNIT: Interacts with LIF1 via its BRCT domain. Interacts with POL4
CC in the DNL4-LIF1 complex. {ECO:0000269|PubMed:12235149,
CC ECO:0000269|PubMed:16388993, ECO:0000269|PubMed:9670033}.
CC -!- INTERACTION:
CC Q08387; 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; Note=Produces 2 separate ORFs.; Evidence={ECO:0000305};
CC Sequence=AAC49485.1; Type=Frameshift; Note=Produces 2 separate ORFs.; Evidence={ECO:0000305};
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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 AlphaFoldDB; Q08387; -.
DR SMR; Q08387; -.
DR BioGRID; 34408; 256.
DR ComplexPortal; CPX-1665; DNA ligase IV complex.
DR DIP; DIP-5801N; -.
DR IntAct; Q08387; 22.
DR STRING; 4932.YOR005C; -.
DR iPTMnet; Q08387; -.
DR PaxDb; Q08387; -.
DR PRIDE; Q08387; -.
DR EnsemblFungi; YOR005C_mRNA; YOR005C; YOR005C.
DR GeneID; 854166; -.
DR KEGG; sce:YOR005C; -.
DR SGD; S000005531; DNL4.
DR VEuPathDB; FungiDB:YOR005C; -.
DR eggNOG; KOG0966; Eukaryota.
DR GeneTree; ENSGT00860000133881; -.
DR HOGENOM; CLU_004844_1_1_1; -.
DR InParanoid; Q08387; -.
DR OMA; EGIMIKH; -.
DR BioCyc; YEAST:G3O-33555-MON; -.
DR BRENDA; 6.5.1.1; 984.
DR EvolutionaryTrace; Q08387; -.
DR PRO; PR:Q08387; -.
DR Proteomes; UP000002311; Chromosome XV.
DR RNAct; Q08387; protein.
DR GO; GO:0032807; C:DNA ligase IV complex; IPI:SGD.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
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; IEA:InterPro.
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 CDD; cd07903; Adenylation_DNA_ligase_IV; 1.
DR Gene3D; 1.10.3260.10; -; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.10190; -; 2.
DR InterPro; IPR044125; Adenylation_DNA_ligase_IV.
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; IPR036599; DNA_ligase_N_sf.
DR InterPro; IPR029710; LIG4.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR PANTHER; PTHR45997; PTHR45997; 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; 1.
DR SUPFAM; SSF52113; SSF52113; 2.
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; DNA damage;
KW DNA recombination; DNA repair; DNA replication; Ligase; Magnesium;
KW Metal-binding; Nucleotide-binding; Nucleus; Reference proteome; Repeat.
FT CHAIN 1..944
FT /note="DNA ligase 4"
FT /id="PRO_0000059582"
FT DOMAIN 681..780
FT /note="BRCT 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT DOMAIN 836..941
FT /note="BRCT 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT ACT_SITE 282
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT BINDING 280
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 287
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 304
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 340
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 442
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 447
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 458
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 464
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="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
