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 03-AUG-2022, entry version 110.
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:P18858};
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; Q90YB1; -.
DR GeneID; 418764; -.
DR KEGG; gga:418764; -.
DR CTD; 3981; -.
DR VEuPathDB; HostDB:geneid_418764; -.
DR eggNOG; KOG0966; Eukaryota.
DR InParanoid; Q90YB1; -.
DR OrthoDB; 274264at2759; -.
DR PhylomeDB; Q90YB1; -.
DR Reactome; R-GGA-353423; Non-homologous end joining (NHEJ).
DR PRO; PR:Q90YB1; -.
DR Proteomes; UP000000539; Unplaced.
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; IBA:GO_Central.
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 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; 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 PANTHER; PTHR45997; PTHR45997; 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; SSF117018; 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 2: Evidence at transcript level;
KW ATP-binding; Cell cycle; Cell division; DNA damage; DNA recombination;
KW DNA repair; DNA replication; Ligase; Magnesium; Metal-binding;
KW Nucleotide-binding; Nucleus; 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 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:P18858"
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 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 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
