ID   DNLI_THEKO              Reviewed;         559 AA.
AC   Q9HHC4; Q5JHF2;
DT   20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT   20-JUN-2001, sequence version 2.
DT   13-SEP-2023, entry version 133.
DE   RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000303|PubMed:11053387};
DE            EC=6.5.1.6 {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000269|PubMed:11053387};
DE   AltName: Full=Lig(Tk) {ECO:0000303|PubMed:11053387};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP/NAD(+)] {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000305};
GN   Name=lig {ECO:0000255|HAMAP-Rule:MF_00407}; OrderedLocusNames=TK2140;
OS   Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS   (Pyrococcus kodakaraensis (strain KOD1)).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=69014;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, FUNCTION,
RP   CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND SUBUNIT.
RC   STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX   PubMed=11053387; DOI=10.1128/jb.182.22.6424-6433.2000;
RA   Nakatani M., Ezaki S., Atomi H., Imanaka T.;
RT   "A DNA ligase from a hyperthermophilic archaeon with unique cofactor
RT   specificity.";
RL   J. Bacteriol. 182:6424-6433(2000).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX   PubMed=15710748; DOI=10.1101/gr.3003105;
RA   Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT   "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT   kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL   Genome Res. 15:352-363(2005).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC       replication, DNA recombination and DNA repair. Can also use NAD, but
CC       less efficiently than ATP. {ECO:0000269|PubMed:11053387}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC         diphosphate.; EC=6.5.1.6; Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC         ECO:0000269|PubMed:11053387};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-
CC         nicotinamide D-nucleotide.; EC=6.5.1.6; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00407, ECO:0000269|PubMed:11053387};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00407, ECO:0000269|PubMed:11053387};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 8.0. {ECO:0000269|PubMed:11053387};
CC       Temperature dependence:
CC         Still active at 100 degrees Celsius. Thermostable.
CC         {ECO:0000269|PubMed:11053387};
CC   -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:11053387}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB15949.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC       Sequence=BAD86329.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; AB042527; BAB15949.1; ALT_INIT; Genomic_DNA.
DR   EMBL; AP006878; BAD86329.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_048053886.1; NC_006624.1.
DR   AlphaFoldDB; Q9HHC4; -.
DR   SMR; Q9HHC4; -.
DR   STRING; 69014.TK2140; -.
DR   EnsemblBacteria; BAD86329; BAD86329; TK2140.
DR   GeneID; 78448677; -.
DR   KEGG; tko:TK2140; -.
DR   PATRIC; fig|69014.16.peg.2096; -.
DR   eggNOG; arCOG01347; Archaea.
DR   HOGENOM; CLU_005138_6_0_2; -.
DR   InParanoid; Q9HHC4; -.
DR   OrthoDB; 31274at2157; -.
DR   PhylomeDB; Q9HHC4; -.
DR   BRENDA; 6.5.1.1; 5246.
DR   Proteomes; UP000000536; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
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:0006266; P:DNA ligation; IBA:GO_Central.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR   GO; GO:0006273; P:lagging strand elongation; IBA:GO_Central.
DR   CDD; cd07901; Adenylation_DNA_ligase_Arch_LigB; 1.
DR   CDD; cd07972; OBF_DNA_ligase_Arch_LigB; 1.
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   HAMAP; MF_00407; DNA_ligase; 1.
DR   InterPro; IPR022865; DNA_ligae_ATP-dep_bac/arc.
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; IPR012340; NA-bd_OB-fold.
DR   NCBIfam; TIGR00574; dnl1; 1.
DR   PANTHER; PTHR45674:SF7; DNA LIGASE; 1.
DR   PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 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; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR   PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Cell cycle; Cell division; Direct protein sequencing;
KW   DNA damage; DNA recombination; DNA repair; DNA replication; Ligase;
KW   Magnesium; Metal-binding; NAD; Nucleotide-binding; Reference proteome.
FT   CHAIN           1..559
FT                   /note="DNA ligase"
FT                   /id="PRO_0000059615"
FT   ACT_SITE        249
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         247
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         254
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         269
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         299
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         339
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         414
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         420
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
SQ   SEQUENCE   559 AA;  63749 MW;  91AB32542E03D20D CRC64;
     MRYSELADLY RRLEKTTLKT LKTKFVADFL KKTPDELLEI VPYLILGKVF PDWDERELGV
     GEKLLIKAVS MATGVPEKEI EDSVRDTGDL GESVALAIKK KKQKSFFSQP LTIKRVYDTF
     VKIAEAQGEG SQDRKMKYLA NLFMDAEPEE GKYLARTVLG TMRTGVAEGI LRDAIAEAFR
     VKPELVERAY MLTSDFGYVA KIAKLEGNEG LSKVRIQIGK PIRPMLAQNA ASVKDALIEM
     GGEAAFEIKY DGARVQVHKD GDKVIVYSRR LENVTRSIPE VIEAIKAALK PEKAIVEGEL
     VAVGENGRPR PFQYVLRRFR RKYNIDEMIE KIPLELNLFD VMFVDGESLI ETKFIDRRNK
     LEEIVKESEK IKLAEQLITK KVEEAEAFYR RALELGHEGL MAKRLDSIYE PGNRGKKWLK
     IKPTMENLDL VIIGAEWGEG RRAHLLGSFL VAAYDPHSGE FLPVGKVGSG FTDEDLVEFT
     KMLKPYIVRQ EGKFVEIEPK FVIEVTYQEI QKSPKYKSGF ALRFPRYVAL REDKSPEEAD
     TIERVAELYE LQERFKAKK
//