ID   DNLI_HYPBU              Reviewed;         608 AA.
AC   A2BJX6;
DT   03-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT   20-FEB-2007, sequence version 1.
DT   27-MAR-2024, entry version 99.
DE   RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000303|PubMed:23546841};
DE            EC=6.5.1.7 {ECO:0000269|PubMed:23546841};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP/ADP/GTP] {ECO:0000305};
GN   Name=lig {ECO:0000255|HAMAP-Rule:MF_00407};
GN   OrderedLocusNames=Hbut_0421;
OS   Hyperthermus butylicus (strain DSM 5456 / JCM 9403 / PLM1-5).
OC   Archaea; Thermoproteota; Thermoprotei; Desulfurococcales; Pyrodictiaceae;
OC   Hyperthermus.
OX   NCBI_TaxID=415426;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 5456 / JCM 9403 / PLM1-5;
RX   PubMed=17350933; DOI=10.1155/2007/745987;
RA   Bruegger K., Chen L., Stark M., Zibat A., Redder P., Ruepp A., Awayez M.,
RA   She Q., Garrett R.A., Klenk H.-P.;
RT   "The genome of Hyperthermus butylicus: a sulfur-reducing, peptide
RT   fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C.";
RL   Archaea 2:127-135(2007).
RN   [2]
RP   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC   STRAIN=DSM 5456 / JCM 9403 / PLM1-5;
RX   PubMed=23546841; DOI=10.1007/s00792-013-0536-6;
RA   Kim J.H., Lee K.K., Sun Y., Seo G.J., Cho S.S., Kwon S.H., Kwon S.T.;
RT   "Broad nucleotide cofactor specificity of DNA ligase from the
RT   hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary
RT   significance.";
RL   Extremophiles 17:515-522(2013).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC       replication, DNA recombination and DNA repair. Can use ATP, ADP and
CC       GTP, but not CTP, TTP or NAD(+). {ECO:0000269|PubMed:23546841}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC         diphosphate.; EC=6.5.1.7; Evidence={ECO:0000255|HAMAP-Rule:MF_00407,
CC         ECO:0000269|PubMed:23546841};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ADP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + phosphate.;
CC         EC=6.5.1.7; Evidence={ECO:0000269|PubMed:23546841};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=GTP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + GMP +
CC         diphosphate.; EC=6.5.1.7; Evidence={ECO:0000269|PubMed:23546841};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:23546841};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:23546841};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 8.0. {ECO:0000269|PubMed:23546841};
CC       Temperature dependence:
CC         Optimum temperature is 75 degrees Celsius.
CC         {ECO:0000269|PubMed:23546841};
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000305}.
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DR   EMBL; CP000493; ABM80287.1; -; Genomic_DNA.
DR   RefSeq; WP_011821605.1; NC_008818.1.
DR   AlphaFoldDB; A2BJX6; -.
DR   SMR; A2BJX6; -.
DR   STRING; 415426.Hbut_0421; -.
DR   EnsemblBacteria; ABM80287; ABM80287; Hbut_0421.
DR   GeneID; 4781994; -.
DR   KEGG; hbu:Hbut_0421; -.
DR   eggNOG; arCOG01347; Archaea.
DR   HOGENOM; CLU_005138_6_0_2; -.
DR   OrthoDB; 31274at2157; -.
DR   Proteomes; UP000002593; 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:0005525; F:GTP binding; IEA:UniProtKB-KW.
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; cd07969; OBF_DNA_ligase_I; 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; DNA LIGASE 1/3 FAMILY MEMBER; 1.
DR   PANTHER; PTHR45674:SF9; DNA LIGASE 3; 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; DNA damage; DNA recombination;
KW   DNA repair; DNA replication; GTP-binding; Ligase; Magnesium; Manganese;
KW   Metal-binding; Nucleotide-binding; Reference proteome.
FT   CHAIN           1..608
FT                   /note="DNA ligase"
FT                   /id="PRO_0000365248"
FT   ACT_SITE        268
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         266
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         273
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         288
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         318
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         358
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         435
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         441
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
SQ   SEQUENCE   608 AA;  68330 MW;  7D16CF4AEB60771E CRC64;
     MSMPFSVLAE TFEKLERVTA RTQMLLYLVE LFKKTPPEII DKVVYFIQGK LWPDWKGLPE
     LGIGEKMLIK AASIALHVSE KQIEQLVKKL GDTGKAIEMI KREKQQKQKA VGLLAFMQKP
     SGGESTLTVE KVYDTLARIA LVQGEGSRDI KLKLLAGLLA EASPREAKYI ARFVEGRLRL
     GVGDATIMEA LAVVYGGSAA MRSVVERAYN LRADLGMVAK ILATQGIDAL KNIKPEVGVP
     IRPMLAERLN DPVEIIKKLG GRALVEYKYD GERAQIHKKG DKIWIFSRRL ENITHMYPDV
     VEMAKKGIKA EEAIVEGEIV AIDPETGEFR PFQVLMHRRR KKDVHAVLSE IPVAVFLFDT
     LYVNGEDLTL KPLPARHEVL EKIIEQSDTW RIAEGIVTSD PQELESFFLK AIEDGAEGVM
     AKAIHDRSIY QAGARGWLWI KYKRDYKSEM SDTVDLVVIG AFYGKGRRGG KFGALLMAAY
     DPDTDTFKSV CKVGSGFTDE DLERLDDMLK PYISDKKPAR VDSQMKPDVW VEPTLVAEII
     GAELTLSPIH TCCYGWVKSG AGISIRFPRF IRWRPDKGPE DATTTKELYE MYKRQLRRIK
     EEEAPTGV
//