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Database: UniProt/SWISS-PROT
Entry: DNLI_STAMF
LinkDB: DNLI_STAMF
Original site: 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   05-DEC-2018, entry version 76.
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 /
OS   F1).
OC   Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC   Desulfurococcaceae; Staphylothermus.
OX   NCBI_TaxID=399550;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY,
RP   COFACTOR, 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.,
RA   Kwon S.T.;
RT   "Cloning and expression of a DNA ligase from the hyperthermophilic
RT   archaeon 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.,
RA   Mukhopadhyay B., 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.,
RA   Huber H., Kyrpides N.C.;
RT   "Complete genome sequence of Staphylothermus marinus Stetter and Fiala
RT   1986 type strain F1.";
RL   Stand. Genomic Sci. 1:183-188(2009).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA
CC       during DNA replication, DNA recombination and DNA repair. Can use
CC       both ATP and 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-
CC         Rule:MF_00407, ECO:0000269|PubMed:17118474};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ADP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP +
CC         phosphate.; 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;
CC         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=Translation N-terminally shortened.; Evidence={ECO:0000305};
CC       Sequence=ABN70409.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
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   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   eggNOG; COG1793; LUCA.
DR   HOGENOM; HOG000036008; -.
DR   KO; K10747; -.
DR   OrthoDB; POG093Z03L0; -.
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:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniRule.
DR   Gene3D; 1.10.3260.10; -; 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; Complete proteome; DNA damage;
KW   DNA recombination; DNA repair; DNA replication; Ligase; Magnesium;
KW   Manganese; Metal-binding; Nucleotide-binding; Reference proteome.
FT   CHAIN         1    597       DNA ligase.
FT                                /FTId=PRO_0000365264.
FT   ACT_SITE    264    264       N6-AMP-lysine intermediate.
FT                                {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     262    262       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     269    269       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     284    284       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     314    314       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     354    354       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     431    431       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     437    437       ATP. {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
//
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