DNLI_HYPBU
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 03-AUG-2022, entry version 94.
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}; OrderedLocusNames=Hbut_0421;
OS Hyperthermus butylicus (strain DSM 5456 / JCM 9403 / PLM1-5).
OC Archaea; Crenarchaeota; 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 OMA; WIKYKRD; -.
DR OrthoDB; 52275at2157; -.
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 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; 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
