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   27-MAR-2024, entry version 118.
DE   RecName: Full=DNA ligase 4;
DE            EC=6.5.1.1 {ECO:0000250|UniProtKB:Q08387};
DE   AltName: Full=DNA ligase IV;
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] 4;
GN   Name=lig4; ORFNames=DDB_G0292760;
OS   Dictyostelium discoideum (Social amoeba).
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: DNA ligase involved in DNA non-homologous end joining (NHEJ);
CC       required for double-strand break (DSB) repair.
CC       {ECO:0000250|UniProtKB:Q08387}.
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:Q08387};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000250|UniProtKB:P49917};
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q08387}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000305}.
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DR   EMBL; AAFI02000196; EAL61054.1; -; Genomic_DNA.
DR   RefSeq; XP_629472.1; XM_629470.1.
DR   AlphaFoldDB; Q54CR9; -.
DR   SMR; Q54CR9; -.
DR   STRING; 44689.Q54CR9; -.
DR   PaxDb; 44689-DDB0232255; -.
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: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   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; 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; 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; PS50160; DNA_LIGASE_A3; 1.
PE   3: Inferred from homology;
KW   ATP-binding; DNA damage; DNA recombination; DNA repair; Ligase; Magnesium;
KW   Metal-binding; Nucleotide-binding; Nucleus; 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:P49917"
FT   BINDING         416
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
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         514
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         574
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
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"
FT   BINDING         598
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
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
//