ID   B7R216_9EURY            Unreviewed;       562 AA.
AC   B7R216;
DT   10-FEB-2009, integrated into UniProtKB/TrEMBL.
DT   10-FEB-2009, sequence version 1.
DT   24-JAN-2024, entry version 70.
DE   RecName: Full=DNA ligase {ECO:0000256|ARBA:ARBA00013308, ECO:0000256|HAMAP-Rule:MF_00407};
DE            EC=6.5.1.6 {ECO:0000256|HAMAP-Rule:MF_00407};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP/NAD(+)] {ECO:0000256|HAMAP-Rule:MF_00407};
GN   Name=lig {ECO:0000256|HAMAP-Rule:MF_00407};
GN   ORFNames=TAM4_1751 {ECO:0000313|EMBL:EEB74384.1};
OS   Thermococcus sp. AM4.
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=246969 {ECO:0000313|EMBL:EEB74384.1, ECO:0000313|Proteomes:UP000009277};
RN   [1] {ECO:0000313|EMBL:EEB74384.1, ECO:0000313|Proteomes:UP000009277}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AM4 {ECO:0000313|EMBL:EEB74384.1,
RC   ECO:0000313|Proteomes:UP000009277};
RX   PubMed=22123768; DOI=10.1128/JB.06259-11;
RA   Oger P., Sokolova T.G., Kozhevnikova D.A., Chernyh N.A., Bartlett D.H.,
RA   Bonch-Osmolovskaya E.A., Lebedinsky A.V.;
RT   "Complete Genome Sequence of the Hyperthermophilic Archaeon Thermococcus
RT   sp. Strain AM4, Capable of Organotrophic Growth and Growth at the Expense
RT   of Hydrogenogenic or Sulfidogenic Oxidation of Carbon Monoxide.";
RL   J. Bacteriol. 193:7019-7020(2011).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC       replication, DNA recombination and DNA repair. {ECO:0000256|HAMAP-
CC       Rule:MF_00407}.
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:0000256|HAMAP-Rule:MF_00407};
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:0000256|HAMAP-
CC         Rule:MF_00407};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_00407};
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000256|HAMAP-Rule:MF_00407, ECO:0000256|RuleBase:RU004196}.
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DR   EMBL; CP002952; EEB74384.1; -; Genomic_DNA.
DR   AlphaFoldDB; B7R216; -.
DR   STRING; 246969.TAM4_1751; -.
DR   KEGG; tha:TAM4_1751; -.
DR   eggNOG; arCOG01347; Archaea.
DR   HOGENOM; CLU_005138_6_0_2; -.
DR   Proteomes; UP000009277; 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; IEA:UniProtKB-UniRule.
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:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniRule.
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   3: Inferred from homology;
KW   ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW   Rule:MF_00407};
KW   Cell cycle {ECO:0000256|ARBA:ARBA00023306, ECO:0000256|HAMAP-
KW   Rule:MF_00407};
KW   Cell division {ECO:0000256|ARBA:ARBA00022618, ECO:0000256|HAMAP-
KW   Rule:MF_00407};
KW   DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW   Rule:MF_00407};
KW   DNA recombination {ECO:0000256|ARBA:ARBA00023172, ECO:0000256|HAMAP-
KW   Rule:MF_00407};
KW   DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW   Rule:MF_00407};
KW   DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP-
KW   Rule:MF_00407};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00407};
KW   Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00407};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_00407}; NAD {ECO:0000256|HAMAP-Rule:MF_00407};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW   Rule:MF_00407}.
FT   DOMAIN          330..458
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   ACT_SITE        252
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         250
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         257
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         272
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         302
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         342
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         417
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         423
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
SQ   SEQUENCE   562 AA;  63935 MW;  516DF59572BDE926 CRC64;
     MGDMKYLELA ELYRRLEKTT LKTLKTKFVA DFLKKTPDDL LEIVPYLILG KVFPDWDERE
     LGVGEKLLIR AVSMATGVPE KEIENSIKDT GDLGESVALA LKKRKQKSFF SQPLTIKRVY
     NTFVKVAEAS GEGSQDRKMK YLANLFMDAT PEEGKYLART VLGTMRTGVA EGILRDAIAE
     AFKVKPELVE RAYMLTSDFG YVTRVAKLEG NEGLSKVSIQ IGKPIRPMLA QNAANVKEAL
     IEMGGEAAFE IKYDGARVQV HRDGDRVIIY SRRLENVTRS IPEIVEAVKA SLRPSKVIVE
     GELVAVGENG RPRPFQYVLR RFRRKYNIEE MIEKIPLELN LFDILYVEGE SLIDTKFAER
     RKKLEESVEE SDKIKLAEQL VTKKVDEAEE FYKRALELGH EGLMAKRLDS VYEPGNRGKK
     WLKIKPTMEN LDLVIIGAEW GEGRRAHLLG SFLVAAYDPE SGEFVPVGKV GSGFTDEDLI
     EFTKMLKPLI VREEGKFVEI QPKVVIEVTY QEIQKSPKYK SGFALRFPRY VALREDKSPE
     EADTIERVAQ LYELQEKFKA KR
//