DNLI_THEKO
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 03-AUG-2022, entry version 129.
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;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC 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; 3235455; -.
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; 52275at2157; -.
DR PhylomeDB; Q9HHC4; -.
DR BRENDA; 6.5.1.1; 5246.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
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 Gene3D; 1.10.3260.10; -; 1.
DR Gene3D; 2.40.50.140; -; 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 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; SSF117018; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR TIGRFAMs; TIGR00574; dnl1; 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
