ID   DNLI4_CRYNJ             Reviewed;        1065 AA.
AC   P0CN08; Q55JS6; Q5K9S5;
DT   28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 1.
DT   27-MAR-2024, entry version 61.
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; OrderedLocusNames=CNK00930;
OS   Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC
OS   MYA-565) (Filobasidiella neoformans).
OC   Eukaryota; Fungi; Dikarya; Basidiomycota; Agaricomycotina; Tremellomycetes;
OC   Tremellales; Cryptococcaceae; Cryptococcus;
OC   Cryptococcus neoformans species complex.
OX   NCBI_TaxID=214684;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=JEC21 / ATCC MYA-565;
RX   PubMed=15653466; DOI=10.1126/science.1103773;
RA   Loftus B.J., Fung E., Roncaglia P., Rowley D., Amedeo P., Bruno D.,
RA   Vamathevan J., Miranda M., Anderson I.J., Fraser J.A., Allen J.E.,
RA   Bosdet I.E., Brent M.R., Chiu R., Doering T.L., Donlin M.J., D'Souza C.A.,
RA   Fox D.S., Grinberg V., Fu J., Fukushima M., Haas B.J., Huang J.C.,
RA   Janbon G., Jones S.J.M., Koo H.L., Krzywinski M.I., Kwon-Chung K.J.,
RA   Lengeler K.B., Maiti R., Marra M.A., Marra R.E., Mathewson C.A.,
RA   Mitchell T.G., Pertea M., Riggs F.R., Salzberg S.L., Schein J.E.,
RA   Shvartsbeyn A., Shin H., Shumway M., Specht C.A., Suh B.B., Tenney A.,
RA   Utterback T.R., Wickes B.L., Wortman J.R., Wye N.H., Kronstad J.W.,
RA   Lodge J.K., Heitman J., Davis R.W., Fraser C.M., Hyman R.W.;
RT   "The genome of the basidiomycetous yeast and human pathogen Cryptococcus
RT   neoformans.";
RL   Science 307:1321-1324(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:0000255|PROSITE-
CC         ProRule:PRU10135};
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; AE017351; AAW46139.1; -; Genomic_DNA.
DR   RefSeq; XP_567656.1; XM_567656.1.
DR   AlphaFoldDB; P0CN08; -.
DR   SMR; P0CN08; -.
DR   STRING; 214684.P0CN08; -.
DR   PaxDb; 214684-P0CN08; -.
DR   eggNOG; KOG0966; Eukaryota.
DR   HOGENOM; CLU_004844_1_0_1; -.
DR   InParanoid; P0CN08; -.
DR   OMA; DYLWIRD; -.
DR   Proteomes; UP000002149; Chromosome 11.
DR   GO; GO:0032807; C:DNA ligase IV complex; IBA:GO_Central.
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; ISS:UniProtKB.
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:0097680; P:double-strand break repair via classical nonhomologous end joining; ISS:UniProtKB.
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   CDD; cd07903; Adenylation_DNA_ligase_IV; 1.
DR   CDD; cd18435; BRCT_BRC1_like_rpt1; 1.
DR   CDD; cd17722; BRCT_DNA_ligase_IV_rpt1; 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; 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   NCBIfam; TIGR00574; dnl1; 1.
DR   PANTHER; PTHR45997; DNA LIGASE 4; 1.
DR   PANTHER; PTHR45997:SF1; DNA LIGASE 4; 1.
DR   Pfam; PF16589; BRCT_2; 2.
DR   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF04675; DNA_ligase_A_N; 1.
DR   SMART; SM00292; BRCT; 2.
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   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..1065
FT                   /note="DNA ligase 4"
FT                   /id="PRO_0000278381"
FT   DOMAIN          696..775
FT                   /note="BRCT 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   DOMAIN          954..1064
FT                   /note="BRCT 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   REGION          1..20
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          825..928
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        833..866
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        891..907
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        297
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT   BINDING         295
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         297
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         298
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         302
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         357
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         357
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255"
FT   BINDING         387
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         452
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         452
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255"
FT   BINDING         457
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         474
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         476
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
SQ   SEQUENCE   1065 AA;  122466 MW;  7E0AC640AB2D6236 CRC64;
     MAVHAPYNHA PPPTQEINGQ KPTLAPAITL ERPADCINRG QYPAFYIICG YLNRLRADAP
     HKKYELLTRI FGNWREKVGP DLYPLIRLLL PDKDRERPVY NLKESMLARC YIDILSLEKH
     SEAAQRLIKW KQPAGNSPNP TGDFAKVCYN EIKARSTVEE GQLSVEAVNM LLDKLAVGKM
     KQKDYVPILK AINMQCTAEE QEWIIRIILK DLHISIRERG VLSAFHPDAI DLYNVCSDLK
     RVCWTLYDPG FRLNKNETHL ELFHSFLPQL CGRMNDASLE NIAKAIGAPK EFIMEEKLDG
     ERIQLHMRGN GAQWFYCSRK AKDYTYLYGA HPGEGSLTRY IATAFQDNVR NVILDGEMMV
     WDPVVERYLA FGTLKSAALA FSLVKVFDIL FLNDHCLSRK RLSERKRLLR SGKIFKNIEN
     YKGRLEFVDE KRGKNAKDIR EYLERVVETK GEGLVVKKTD VIYQTNSRGY DWIKVKPEYS
     DQMGENLEVL VLGGWWGKGG RSGKISRLLC GLREQAFDDG TLQDFLFNRF WNELLGLRVD
     FVSHLMHLRS MRCSPTHLSQ CRNKHKKHWR PFDRSNPPPF MKLGPVGLDD KPDVYIEPEN
     SFVIEVKASE IVPAGYGIGF TLRFPRCKYI YYDKNSRDYA LDDECLWTVG QGFFYKTRKL
     IKRTDFMDLF SRPKRSYDDS QGPGNFRGQK LSDADVETSI FSDMTFSDLE ALVHKHGADF
     TQAQLSDLSA IVISPDQKNP LVRAQIRHGV NVIKPEWVFE SIARRTALPF LKEFLVFASE
     EAQDGRYYNK TLEQYDKVSF VRDRTGGALV DEDGDADVED EIMDGEDKDE IDVEESRESK
     NRRMAREDLK EKESNRTLEQ KKLQEAWGLR SRASPGDSDS EPEEEMSLKE ESDTDSERSR
     GLRAIYEDEE DGENDSHESD VGVNGDDYRA VPLSGLNDKE EGLMGESPEA MHYDEDRIFY
     HLAFYIDTAK NAAVNGLESS SPSFDTQERL VKVEKLLIEN GGRVARSISD PKLTHIIMDD
     EDSRRYVELT RKTAMPKRKH IVTPKWVEDC VDEETLLDED LYKPK
//