DNLI4_DICDI
ID DNLI4_DICDI Reviewed; 1088 AA.
AC Q54CR9;
DT 23-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=DNA ligase 4;
DE EC=6.5.1.1;
DE AltName: Full=DNA ligase IV;
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP] 4;
GN Name=lig4; ORFNames=DDB_G0292760;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
CC -!- FUNCTION: Efficiently joins single-strand breaks in a double-stranded
CC polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA
CC nonhomologous end joining (NHEJ) required for double-strand break
CC repair. {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 -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P18858};
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; AAFI02000196; EAL61054.1; -; Genomic_DNA.
DR RefSeq; XP_629472.1; XM_629470.1.
DR AlphaFoldDB; Q54CR9; -.
DR SMR; Q54CR9; -.
DR STRING; 44689.DDB0232255; -.
DR PaxDb; Q54CR9; -.
DR EnsemblProtists; EAL61054; EAL61054; DDB_G0292760.
DR GeneID; 8628862; -.
DR KEGG; ddi:DDB_G0292760; -.
DR dictyBase; DDB_G0292760; lig4.
DR eggNOG; KOG0966; Eukaryota.
DR HOGENOM; CLU_004844_2_0_1; -.
DR InParanoid; Q54CR9; -.
DR OMA; EGIMIKH; -.
DR PhylomeDB; Q54CR9; -.
DR Reactome; R-DDI-5693571; Nonhomologous End-Joining (NHEJ).
DR PRO; PR:Q54CR9; -.
DR Proteomes; UP000002195; Chromosome 6.
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:dictyBase.
DR GO; GO:0005634; C:nucleus; ISS:dictyBase.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; ISS:dictyBase.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; ISS:dictyBase.
DR GO; GO:0046872; F:metal ion binding; 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; IBA:GO_Central.
DR GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR GO; GO:0000012; P:single strand break repair; ISS:dictyBase.
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; 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; PS50160; DNA_LIGASE_A3; 1.
PE 3: Inferred from homology;
KW ATP-binding; DNA damage; DNA recombination; DNA repair; DNA replication;
KW Ligase; Magnesium; Metal-binding; Nucleotide-binding; Nucleus;
KW Reference proteome; Repeat.
FT CHAIN 1..1088
FT /note="DNA ligase 4"
FT /id="PRO_0000351216"
FT DOMAIN 827..917
FT /note="BRCT 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT DOMAIN 984..1088
FT /note="BRCT 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT REGION 1..56
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 73..117
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..16
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 25..56
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 73..91
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 416
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT BINDING 414
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P18858"
FT BINDING 421
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P18858"
FT BINDING 467
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P18858"
FT BINDING 467
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 574
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 579
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P18858"
FT BINDING 596
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P18858"
SQ SEQUENCE 1088 AA; 124791 MW; FE1B3C00A20B5E76 CRC64;
MALSLYYDED DDENENENKD KPNNDFKNQQ QINTSKTTNN NNNINNKNNY NNKFNDDDIF
NNDKIITKPR VTTTTTTTKN TSTNSNINKT KFNDDDIFDD EDEDSNSNKT TTTTTTTTTT
TDTIITNDYR YQKTVPFSSF CDLMNRIIND TKISNKKNYL EKFMNHYKDE PNNFYQLLRL
ILPQLDKDRN SYGLKEKTLA RLYVELLNIS PESVDAMRLL NWKKSTNDEI GGDFGTAVYL
SLKNRCNNDN GRIKVSMGDI NESLDQLSQP LTDKKTKVSI LKKVLRSTTA QEQKWFVRII
LKEMKNGLSD NITLKFFHPD AIDHFNITSN LRLVCTNLFY MTQSKQKELK DKQKLEEKEN
LLKQQQQQQN DLDIYKLEIK LFNPIKPMLA NRQSIDNLSM ILNSAISATQ FVVEKKFDGE
RIQIHKDGEQ VKYFSRNSND STGIYGSMFT PIVKECVLAE RCILDGELIV WDSISQRFED
FGNLKTLALN KDGISGSGDP LGINYGKQLC FIAFDILFVK DQSVMNLPLM QRLMLLKRCV
TIKSKQFEIS EQTTVNSISQ IISLLESAII NREEGLMLKN LHSLYVPAER KDKWVKIKPE
YIDGMGNGAD DLDLVIIGGY YGSGLNRRGG TISHFMLGVP FIADSTDTDI DDESTFDKNV
IFYSFCKVGS GYTDIQLKSL QKDLDPHWNN FSTSKPPSII QLAEPFKEKP DVWIDPRVYS
KVLQIKASQI VVTDKYKCGY TLRFPRVLKI RDDKGWKDCC SHEEIIDLFT NYSTNLNFKR
DHEYGDGSGG KNKKLKKSKK TTNQLLADSG LKVLSIFQDT DTSGIIPTQN IFQGIEICVI
KGSSGEYTKS KLEIMIVEMG GSKVQYPSRN TNYVISSKEV VKIQNLIQSG FIDIVSFNWI
VDCYNEKRLV PLGPKYMIFS TESTKKRFLL DSDQFGDSYI NETTEQSLKD SFNQIDKLKL
KKQLSINSTT TTTTTSISKY FSNCWWSLFK EFTFYLDLYQ VVGEKSTLIE NNNLELSNLN
IQFYGGKISI EFNNKITHVV LDSLDLSRIT FIKNKINSLS LPIQIVTTNW IQLSINNYSI
QPILEILD
