DNLI_STAMF
ID DNLI_STAMF Reviewed; 597 AA.
AC A3DP49; A3E0P8;
DT 03-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 03-MAR-2009, sequence version 2.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000303|PubMed:17118474};
DE EC=6.5.1.7 {ECO:0000305|PubMed:17118474};
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP/ADP] {ECO:0000305};
GN Name=lig {ECO:0000255|HAMAP-Rule:MF_00407}; OrderedLocusNames=Smar_1318;
OS Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Staphylothermus.
OX NCBI_TaxID=399550;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43588 / DSM 3639 / JCM 9404 / F1;
RX PubMed=17118474; DOI=10.1016/j.jbiotec.2006.09.024;
RA Seo M.S., Kim Y.J., Choi J.J., Lee M.S., Kim J.H., Lee J.H., Kwon S.T.;
RT "Cloning and expression of a DNA ligase from the hyperthermophilic archaeon
RT Staphylothermus marinus and properties of the enzyme.";
RL J. Biotechnol. 128:519-530(2007).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43588 / DSM 3639 / JCM 9404 / F1;
RX PubMed=19341479; DOI=10.1186/1471-2164-10-145;
RA Anderson I.J., Dharmarajan L., Rodriguez J., Hooper S., Porat I.,
RA Ulrich L.E., Elkins J.G., Mavromatis K., Sun H., Land M., Lapidus A.,
RA Lucas S., Barry K., Huber H., Zhulin I.B., Whitman W.B., Mukhopadhyay B.,
RA Woese C., Bristow J., Kyrpides N.;
RT "The complete genome sequence of Staphylothermus marinus reveals
RT differences in sulfur metabolism among heterotrophic Crenarchaeota.";
RL BMC Genomics 10:145-145(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43588 / DSM 3639 / JCM 9404 / F1;
RX PubMed=21304655; DOI=10.4056/sigs.30527;
RA Anderson I.J., Sun H., Lapidus A., Copeland A., Glavina Del Rio T.,
RA Tice H., Dalin E., Lucas S., Barry K., Land M., Richardson P., Huber H.,
RA Kyrpides N.C.;
RT "Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986
RT type strain F1.";
RL Stand. Genomic Sci. 1:183-188(2009).
CC -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC replication, DNA recombination and DNA repair. Can use both ATP and
CC ADP. {ECO:0000269|PubMed:17118474}.
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:17118474};
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:17118474};
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:0000250|UniProtKB:A2BJX6};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:17118474};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:17118474};
CC -!- ACTIVITY REGULATION: Inhibited by Ca(2+) and Zn(2+).
CC {ECO:0000269|PubMed:17118474}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.5. {ECO:0000269|PubMed:17118474};
CC Temperature dependence:
CC Optimum temperature is 75 degrees Celsius. Activity declines at
CC temperatures from 75 to 80 degrees Celsius.
CC {ECO:0000269|PubMed:17118474};
CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABE27150.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=ABN70409.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; DQ451010; ABE27150.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP000575; ABN70409.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_011839603.1; NC_009033.1.
DR AlphaFoldDB; A3DP49; -.
DR SMR; A3DP49; -.
DR STRING; 399550.Smar_1318; -.
DR EnsemblBacteria; ABN70409; ABN70409; Smar_1318.
DR GeneID; 4906593; -.
DR KEGG; smr:Smar_1318; -.
DR eggNOG; arCOG01347; Archaea.
DR HOGENOM; CLU_005138_6_0_2; -.
DR OrthoDB; 52275at2157; -.
DR Proteomes; UP000000254; 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 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; Ligase; Magnesium; Manganese; Metal-binding;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1..597
FT /note="DNA ligase"
FT /id="PRO_0000365264"
FT ACT_SITE 264
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT BINDING 262
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 284
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT BINDING 314
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT BINDING 354
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT BINDING 431
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT BINDING 437
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
SQ SEQUENCE 597 AA; 67627 MW; CA4E62C8890515D6 CRC64;
MPFRELADTF ERIEIITSRT QMTVLLVNLF KKTPPEIIDK VVYLLQGRLW PDWKGLPELG
VGEKMLIKAI ALATQSTESE VESLYKSLGD LGKAAEKLKA IYEEKLKKGA MSILAFVPVK
RELTVSQVYE TLSRVALATG EGSRDIKLKL LAGLLSDASP KEAKYIIRFV EGRLRLGIGD
ATIMDALAIV YGGGAHARPI VERAYNLRAD LGHIAKILAT QGLNALKGIK PQVGIPIRPM
LAERLNNPVE ILKKVGGIAF VEYKYDGERA QIHKLGDKIW IYSRRLENIT HQYPDVVDYA
RKYIKANEAI VEGEIVAYDP DTGELRPFQE LMHRKRKHDI HIAIKEVPVK VYLFDLLYVD
GEDYTLKPLP ERRAKLVEII EQTETFQIAE YIRTNNPDEL EKFFLKAIED GAEGVMIKAL
HKNAIYQAGT RGWLWIKYKR DYKSEMIDTV DLVVIGAFYG RGRRGGKYGA LLMASYNPDK
DVFESVCKVG SGFKDEDIDK LPEMLKPYII EHKHPRVVAR MKPDVWVTPA LVAEIIGAEL
TLSPLHTCCL DIIKPGVGIS IRFPRFIRWR PDKGPEDATT SQELLEMYKR QLKKLSE
