ID   DNLI4_NEUCR             Reviewed;        1050 AA.
AC   Q7SB49;
DT   20-FEB-2007, integrated into UniProtKB/Swiss-Prot.
DT   19-MAR-2014, sequence version 2.
DT   27-MAR-2024, entry version 136.
DE   RecName: Full=DNA ligase 4;
DE            EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135};
DE   AltName: Full=DNA ligase IV;
DE   AltName: Full=Mutagen-sensitive protein 53;
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] 4;
GN   Name=mus-53; Synonyms=lig4; ORFNames=NCU06264;
OS   Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 /
OS   FGSC 987).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes;
OC   Sordariomycetidae; Sordariales; Sordariaceae; Neurospora.
OX   NCBI_TaxID=367110;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX   PubMed=17003123; DOI=10.1073/pnas.0604477103;
RA   Ishibashi K., Suzuki K., Ando Y., Takakura C., Inoue H.;
RT   "Nonhomologous chromosomal integration of foreign DNA is completely
RT   dependent on MUS-53 (human Lig4 homolog) in Neurospora.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:14871-14876(2006).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987;
RX   PubMed=12712197; DOI=10.1038/nature01554;
RA   Galagan J.E., Calvo S.E., Borkovich K.A., Selker E.U., Read N.D.,
RA   Jaffe D.B., FitzHugh W., Ma L.-J., Smirnov S., Purcell S., Rehman B.,
RA   Elkins T., Engels R., Wang S., Nielsen C.B., Butler J., Endrizzi M.,
RA   Qui D., Ianakiev P., Bell-Pedersen D., Nelson M.A., Werner-Washburne M.,
RA   Selitrennikoff C.P., Kinsey J.A., Braun E.L., Zelter A., Schulte U.,
RA   Kothe G.O., Jedd G., Mewes H.-W., Staben C., Marcotte E., Greenberg D.,
RA   Roy A., Foley K., Naylor J., Stange-Thomann N., Barrett R., Gnerre S.,
RA   Kamal M., Kamvysselis M., Mauceli E.W., Bielke C., Rudd S., Frishman D.,
RA   Krystofova S., Rasmussen C., Metzenberg R.L., Perkins D.D., Kroken S.,
RA   Cogoni C., Macino G., Catcheside D.E.A., Li W., Pratt R.J., Osmani S.A.,
RA   DeSouza C.P.C., Glass N.L., Orbach M.J., Berglund J.A., Voelker R.,
RA   Yarden O., Plamann M., Seiler S., Dunlap J.C., Radford A., Aramayo R.,
RA   Natvig D.O., Alex L.A., Mannhaupt G., Ebbole D.J., Freitag M., Paulsen I.,
RA   Sachs M.S., Lander E.S., Nusbaum C., Birren B.W.;
RT   "The genome sequence of the filamentous fungus Neurospora crassa.";
RL   Nature 422:859-868(2003).
CC   -!- FUNCTION: DNA ligase involved in DNA non-homologous end joining (NHEJ);
CC       required for double-strand break (DSB) repair.
CC       {ECO:0000269|PubMed:17003123}.
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}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAF34364.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AB261106; BAF34364.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CM002238; EAA33632.2; -; Genomic_DNA.
DR   RefSeq; XP_962868.2; XM_957775.2.
DR   AlphaFoldDB; Q7SB49; -.
DR   SMR; Q7SB49; -.
DR   STRING; 367110.Q7SB49; -.
DR   PaxDb; 5141-EFNCRP00000006048; -.
DR   EnsemblFungi; EAA33632; EAA33632; NCU06264.
DR   GeneID; 3879007; -.
DR   KEGG; ncr:NCU06264; -.
DR   VEuPathDB; FungiDB:NCU06264; -.
DR   HOGENOM; CLU_004844_1_1_1; -.
DR   InParanoid; Q7SB49; -.
DR   OrthoDB; 8251at2759; -.
DR   Proteomes; UP000001805; Chromosome 3, Linkage Group III.
DR   GO; GO:0000785; C:chromatin; IEA:EnsemblFungi.
DR   GO; GO:0032807; C:DNA ligase IV complex; IBA:GO_Central.
DR   GO; GO:0005730; C:nucleolus; IEA:EnsemblFungi.
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; 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; 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; 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   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; 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..1050
FT                   /note="DNA ligase 4"
FT                   /id="PRO_0000278384"
FT   DOMAIN          742..840
FT                   /note="BRCT 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   DOMAIN          936..1049
FT                   /note="BRCT 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   REGION          1..22
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          691..711
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..19
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        331
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT   BINDING         329
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         331
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         332
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         336
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         398
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         398
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255"
FT   BINDING         438
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         498
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         498
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255"
FT   BINDING         503
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         520
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
FT   BINDING         522
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250|UniProtKB:P49917"
SQ   SEQUENCE   1050 AA;  119433 MW;  CDA8E04CF37AFA99 CRC64;
     MNTNRRSRSP DEEALEEDQH QYGAGTLSLE ELDEHFPNRP RNHSKTFPFS DLFRTLFNPL
     IDCKPSTSGG TVRGPKPGRG GHFSKVSYHE QRRHIIERFM SRWRSEVGND FYPAMRLILP
     DKDRDRGVYG LKENTIGKLL VKVMKIDRNS EDGYNLMHWK LPGGQSGVSR SVGDFAGRCL
     EVVSKRAMRA QPGDLTIADV NVLLDRLAAA SGEAEQLPIF EEFYRQMNAE EMMWLVRIIL
     KDMRVGATER TFLNLWHPDA EALFSVSSSL RRVCWELFDP EFRLEQQETG IKLMQCFQPQ
     LAQFQMTTTW EKLVKNLGVT EENPEFWIEE KLDGERMQMH MIEDDTVPGG FRFAFWSRKA
     KDYTYLYGES LGDEQSALTR HLHKAFDDGV RNLILDGEMI TWDIDIDKMV PFGTLKTAAL
     EQQKNPSKAG PRPLYRVFDI LLLNDKPLTE YTLNDRRRAL ERAVVGVHRR LEILPFERAT
     SPDAIEPLLR RVVAEASEGL VLKNPRSRYS LNSRNNDWIK VKPEYMSDFG ESLDCVVVGG
     YFGSGRRGGT LSSFLCGVRV SQNFIKSGNA SAEKCLSFVK VGGGFKAEDY AEIRHHTEGK
     WQDWDPSSPP TEYIELGGGE KLQYEKPDVW IRPSDSVVIS VKAASITQSD QFAMGWTLRF
     PRFRKLRLDR AWDSALDMDE FEVLRSKIKD QEQERKKMEM ENRKRKPATK RARKDLVIAG
     MSDPSSSSAA TPVIAPKETR EASKRLFEGL DFCVLSDSLK PNKMTKPALE KLIKDHGGRI
     HQQVMDHSGQ GKIIIPIADK NVIKVASLRK ANPEMDIIRP KWIFDCLVQP MPFTKQKENK
     KGYLLPFEPT HLFHSGSEET SEEAEQAVDK FGDSYAGDLA DINELKAIME GMESDDYVSD
     SDWDSDSGRG RGGGDGFDMN HFLDHLEEQG TSLDDLRSFM FRRCRVFFAL PSAGNGDGAA
     ESKALRLKNY IRFGNGKVVD ELETATHVVV VTAPLGESSK KEEREIAAEL RYKISLREMG
     SPMPRIVKGE WVEDSWKEGT VVDEEEYVAG
//