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   27-MAR-2024, entry version 92.
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};
GN   OrderedLocusNames=Smar_1318;
OS   Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1).
OC   Archaea; Thermoproteota; 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   AlphaFoldDB; A3DP49; -.
DR   SMR; A3DP49; -.
DR   STRING; 399550.Smar_1318; -.
DR   KEGG; smr:Smar_1318; -.
DR   eggNOG; arCOG01347; Archaea.
DR   HOGENOM; CLU_005138_6_0_2; -.
DR   OrthoDB; 31274at2157; -.
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   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; 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
//