GenomeNet

Database: UniProt/SWISS-PROT
Entry: DNLI4_CHICK
LinkDB: DNLI4_CHICK
Original site: DNLI4_CHICK 
ID   DNLI4_CHICK             Reviewed;         912 AA.
AC   Q90YB1; Q5ZKM3;
DT   07-FEB-2006, integrated into UniProtKB/Swiss-Prot.
DT   07-FEB-2006, sequence version 2.
DT   24-JAN-2024, entry version 115.
DE   RecName: Full=DNA ligase 4 {ECO:0000305};
DE            EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135};
DE   AltName: Full=DNA ligase IV {ECO:0000303|PubMed:11593023};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] 4;
GN   Name=LIG4 {ECO:0000303|PubMed:11593023};
GN   ORFNames=RCJMB04_10b2 {ECO:0000303|PubMed:11593023};
OS   Gallus gallus (Chicken).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC   Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC   Phasianinae; Gallus.
OX   NCBI_TaxID=9031;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=11593023; DOI=10.1073/pnas.201271098;
RA   Adachi N., Ishino T., Ishii Y., Takeda S., Koyama H.;
RT   "DNA ligase IV-deficient cells are more resistant to ionizing radiation in
RT   the absence of Ku70: implications for DNA double-strand break repair.";
RL   Proc. Natl. Acad. Sci. U.S.A. 98:12109-12113(2001).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=CB; TISSUE=Bursa of Fabricius;
RX   PubMed=15642098; DOI=10.1186/gb-2004-6-1-r6;
RA   Caldwell R.B., Kierzek A.M., Arakawa H., Bezzubov Y., Zaim J., Fiedler P.,
RA   Kutter S., Blagodatski A., Kostovska D., Koter M., Plachy J., Carninci P.,
RA   Hayashizaki Y., Buerstedde J.-M.;
RT   "Full-length cDNAs from chicken bursal lymphocytes to facilitate gene
RT   function analysis.";
RL   Genome Biol. 6:R6.1-R6.9(2005).
CC   -!- FUNCTION: DNA ligase involved in DNA non-homologous end joining (NHEJ);
CC       required for double-strand break (DSB) repair and V(D)J recombination.
CC       Catalyzes the NHEJ ligation step of the broken DNA during DSB repair by
CC       resealing the DNA breaks after the gap filling is completed. Joins
CC       single-strand breaks in a double-stranded polydeoxynucleotide in an
CC       ATP-dependent reaction. LIG4 is mechanistically flexible: it can ligate
CC       nicks as well as compatible DNA overhangs alone, while in the presence
CC       of XRCC4, it can ligate ends with 2-nucleotides (nt) microhomology and
CC       1-nt gaps. Forms a subcomplex with XRCC4; the LIG4-XRCC4 subcomplex is
CC       responsible for the NHEJ ligation step and XRCC4 enhances the joining
CC       activity of LIG4. {ECO:0000250|UniProtKB:P49917}.
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:0000250|UniProtKB:P49917,
CC         ECO:0000255|PROSITE-ProRule:PRU10135};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000250|UniProtKB:P49917};
CC   -!- SUBUNIT: Interacts with XRCC4; the LIG4-XRCC4 subcomplex has a 1:2
CC       stoichiometry (By similarity). Component of the core long-range non-
CC       homologous end joining (NHEJ) complex (also named DNA-PK complex)
CC       composed of PRKDC, LIG4, XRCC4, XRCC6/Ku70, XRCC5/Ku86 and NHEJ1/XLF
CC       (By similarity). Additional component of the NHEJ complex includes PAXX
CC       (By similarity). Following autophosphorylation, PRKDC dissociates from
CC       DNA, leading to formation of the short-range NHEJ complex, composed of
CC       LIG4, XRCC4, XRCC6/Ku70, XRCC5/Ku86 and NHEJ1/XLF (By similarity).
CC       {ECO:0000250|UniProtKB:P49917}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P49917}.
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; AB058600; BAB68506.1; -; Genomic_DNA.
DR   EMBL; AJ720061; CAG31720.1; -; mRNA.
DR   RefSeq; NP_001025987.1; NM_001030816.1.
DR   AlphaFoldDB; Q90YB1; -.
DR   SMR; Q90YB1; -.
DR   STRING; 9031.ENSGALP00000027179; -.
DR   PaxDb; 9031-ENSGALP00000027179; -.
DR   GeneID; 418764; -.
DR   KEGG; gga:418764; -.
DR   CTD; 3981; -.
DR   VEuPathDB; HostDB:geneid_418764; -.
DR   eggNOG; KOG0966; Eukaryota.
DR   InParanoid; Q90YB1; -.
DR   OrthoDB; 8251at2759; -.
DR   PhylomeDB; Q90YB1; -.
DR   Reactome; R-GGA-353423; Non-homologous end joining (NHEJ).
DR   PRO; PR:Q90YB1; -.
DR   Proteomes; UP000000539; Unassembled WGS sequence.
DR   GO; GO:0032807; C:DNA ligase IV complex; IBA:GO_Central.
DR   GO; GO:0005958; C:DNA-dependent protein kinase-DNA ligase 4 complex; ISS:UniProtKB.
DR   GO; GO:0070419; C:nonhomologous end joining complex; ISS:UniProtKB.
DR   GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
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; IBA:GO_Central.
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:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IBA:GO_Central.
DR   GO; GO:0033152; P:immunoglobulin V(D)J recombination; IBA:GO_Central.
DR   GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR   CDD; cd07903; Adenylation_DNA_ligase_IV; 1.
DR   CDD; cd17722; BRCT_DNA_ligase_IV_rpt1; 1.
DR   CDD; cd17717; BRCT_DNA_ligase_IV_rpt2; 1.
DR   CDD; cd07968; OBF_DNA_ligase_IV; 1.
DR   Gene3D; 6.10.250.520; -; 1.
DR   Gene3D; 3.40.50.10190; BRCT domain; 2.
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   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; 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; IPR021536; DNA_ligase_IV_dom.
DR   InterPro; IPR036599; DNA_ligase_N_sf.
DR   InterPro; IPR029710; LIG4.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   NCBIfam; TIGR00574; dnl1; 1.
DR   PANTHER; PTHR45997; DNA LIGASE 4; 1.
DR   PANTHER; PTHR45997:SF1; DNA LIGASE 4; 1.
DR   Pfam; PF00533; BRCT; 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   Pfam; PF11411; DNA_ligase_IV; 1.
DR   SMART; SM00292; BRCT; 2.
DR   SUPFAM; SSF117018; ATP-dependent DNA ligase DNA-binding domain; 1.
DR   SUPFAM; SSF52113; BRCT domain; 2.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 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   2: Evidence at transcript level;
KW   ATP-binding; Cell cycle; Cell division; DNA damage; DNA recombination;
KW   DNA repair; Ligase; Magnesium; Metal-binding; Nucleotide-binding; Nucleus;
KW   Reference proteome; Repeat.
FT   CHAIN           1..912
FT                   /note="DNA ligase 4"
FT                   /id="PRO_0000059579"
FT   DOMAIN          659..748
FT                   /note="BRCT 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   DOMAIN          809..912
FT                   /note="BRCT 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   REGION          615..625
FT                   /note="Required for catalytic activity"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   ACT_SITE        278
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT   BINDING         276
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         277
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         278
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         279
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         283
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P18858"
FT   BINDING         336
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P18858"
FT   BINDING         336
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255"
FT   BINDING         350
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         372
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         432
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         432
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255"
FT   BINDING         437
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P18858"
FT   BINDING         454
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P18858"
FT   BINDING         456
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   CONFLICT        492
FT                   /note="V -> I (in Ref. 1; BAB68506)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   912 AA;  104450 MW;  CBF2899CA76D212D CRC64;
     MASAPVLQPS PKRTVASHVP FADLCSTLER IQTCKSRPEK TKYFKDFLDS WRKFHSALHQ
     KEKDVTDSFY PAMRLILPQL ERERMAYGIK ETMLAKLYIE LLNLPKDGKD AVKLLNYRTP
     TGSRGDAGDF AMIAYFVLKP RSPKRGRLTV EQVNELLDAI ANNNAAKNKG LVKKSLLQLI
     TQSTALEQKW LIRMIIKDLK LGVSQQTIFS IFHPDAAELH NVTTDLEKVC RQLHDPSVSL
     SDVSIMLFSA FKPMLAAIAD VQQIEKQMNN QVFYIETKLD GERMQMHKDG DVYKYFSRNG
     FDYTQQFGAS PVDGSLTPFI HNVFKSDIQN CILDGEMMAY NPETQTFMQK GNKFDIKRMV
     EDSDLQTCFC VFDVLMINDQ KLAHESLSKR YKILSNVFTP LTGRIHVVHK KSARTRKEVI
     DALNEAIDNR EEGIMVKDPM STYKPDKRGE GWLKIKPEYV NGLMDELDLL IVGGYWGKGS
     RGGMMSHFLC AVAETPAPNE KPTVFHSICR VGSGYTMKEL YDLGLKLAKH WKPYNRKDPP
     CNILCGTEKP EMYIEPCNSV IVQIKAAEIV NSDMYKTDCT LRFPRIEKIR EDKEWYECMT
     LDMLEHLRSR AEGKLASKHL YIDEYDEPQE KKRRTVPKVK KVIGIAEQFK APDLSNVNKV
     SSMFEDVEFC VMTGMGRYSK SELESRIAEC GGSVVQNPGP DTYCVIVGAE NVRVKNIIAS
     NKYDVVKAEW LLQCFQSKML VPWQPAFMIH MSPETREHFA REYDCYGDSY TADTDVAQLK
     EVFSRVKDNK KMPLDLIAEL EERYSWNSCK LCIFRGNTIY VDYYAIINKP STKIHGTRLS
     IRALELRFYG AKVVPLLEEG VSHVVIGEDH SRVKEMKALR RMFGKKFKIV SELWVTESVK
     EGVPKNETQF LI
//
DBGET integrated database retrieval system