ID   C6A2U9_THESM            Unreviewed;       560 AA.
AC   C6A2U9;
DT   01-SEP-2009, integrated into UniProtKB/TrEMBL.
DT   01-SEP-2009, sequence version 1.
DT   27-MAR-2024, entry version 87.
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   OrderedLocusNames=TSIB_0885 {ECO:0000313|EMBL:ACS89944.1};
OS   Thermococcus sibiricus (strain DSM 12597 / MM 739).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=604354 {ECO:0000313|EMBL:ACS89944.1, ECO:0000313|Proteomes:UP000009079};
RN   [1] {ECO:0000313|EMBL:ACS89944.1, ECO:0000313|Proteomes:UP000009079}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 12597 / MM 739 {ECO:0000313|Proteomes:UP000009079};
RX   PubMed=19447963; DOI=10.1128/AEM.00718-09;
RA   Mardanov A.V., Ravin N.V., Svetlitchnyi V.A., Beletsky A.V.,
RA   Miroshnichenko M.L., Bonch-Osmolovskaya E.A., Skryabin K.G.;
RT   "Metabolic versatility and indigenous origin of the archaeon Thermococcus
RT   sibiricus, isolated from a siberian oil reservoir, as revealed by genome
RT   analysis.";
RL   Appl. Environ. Microbiol. 75:4580-4588(2009).
RN   [2] {ECO:0007829|PDB:4EQ5}
RP   X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 2-560 IN COMPLEX WITH AMP.
RX   PubMed=22297989; DOI=10.1107/S1744309111050913;
RA   Petrova T.E., Bezsudnova E.Y., Dorokhov B.D., Slutskaya E.S.,
RA   Polyakov K.M., Dorovatovskiy P.V., Ravin N.V., Skryabin K.G.,
RA   Kovalchuk M.V., Popov V.O.;
RT   "Expression, purification, crystallization and preliminary crystallographic
RT   analysis of a thermostable DNA ligase from the archaeon Thermococcus
RT   sibiricus.";
RL   Acta Crystallogr. F Struct. Biol. Commun. 68:163-165(2012).
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; CP001463; ACS89944.1; -; Genomic_DNA.
DR   RefSeq; WP_015849163.1; NC_012883.1.
DR   PDB; 4EQ5; X-ray; 2.85 A; A=2-560.
DR   PDBsum; 4EQ5; -.
DR   AlphaFoldDB; C6A2U9; -.
DR   SMR; C6A2U9; -.
DR   STRING; 604354.TSIB_0885; -.
DR   GeneID; 8095876; -.
DR   KEGG; tsi:TSIB_0885; -.
DR   eggNOG; arCOG01347; Archaea.
DR   HOGENOM; CLU_005138_6_0_2; -.
DR   OrthoDB; 31274at2157; -.
DR   Proteomes; UP000009079; 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   1: Evidence at protein level;
KW   3D-structure {ECO:0007829|PDB:4EQ5};
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}; Reference proteome {ECO:0000313|Proteomes:UP000009079}.
FT   DOMAIN          328..456
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   ACT_SITE        250
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         248
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         248
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         251
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         255
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         255
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         270
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         270
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         300
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         300
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         340
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         340
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         404
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         415
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT                   /evidence="ECO:0007829|PDB:4EQ5"
FT   BINDING         415
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
FT   BINDING         421
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00407"
SQ   SEQUENCE   560 AA;  63448 MW;  3B20F1C68A04EDA8 CRC64;
     MLYKELVELY KRLEKTTLKT LKTKFVSDFL KSVEKPELLE VIPYLILGKV FPDWDERELG
     IGEKLLIKAV SMATGINSEE IENSVRDTGD LGESIALALN KRKQKSFFSQ PLTIERVYNT
     LVKIAEASGA GSQDRKLKYL ANLFMDASPD EGKYLARTVL GIMRTGVAEG LLRDALADAF
     KVRVELVERA YMLTSDFGFV AKVAKLEGDE GLAKVKIQVG KPIKPMLAQM AANVREALVE
     MGGEAEFEIK YDGARVQVHK NGNKVLIYSR RLENVTKSIP EVVERVKEAL KPEKVIVEGE
     LVAVEETGRP RPFQYVLRRF RRKYNIEEMI EKIPLELNLF DILYVDGQNM IDTPFMERRK
     VLESVVNSNE WIKSAENLIT KSPEEAEAFY HKALDLGHEG LMAKRLDSTY EPGNRGKKWL
     KIKPTMENLD LVVLGAEWGE GRRSGVLSSF LLGAYDPVKG DFVPVGKVGS GFTDEDLVEF
     TKMLKPLIKK EHGKEVELEP KVVIEVAYQE IQKSPKYESG FALRFPRYIA LREDKGPEDA
     DTVQRLAELY QFQERLKGGR
//