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DNLJ_GEOSE
ID   DNLJ_GEOSE              Reviewed;         670 AA.
AC   O87703;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1998, sequence version 1.
DT   03-AUG-2022, entry version 117.
DE   RecName: Full=DNA ligase {ECO:0000255|HAMAP-Rule:MF_01588};
DE            EC=6.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE   AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000255|HAMAP-Rule:MF_01588};
GN   Name=ligA {ECO:0000255|HAMAP-Rule:MF_01588}; Synonyms=lig;
OS   Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX   NCBI_TaxID=1422;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 29609 / DSM 2027 / NCA 1503 / NCIMB 8924;
RX   PubMed=10407164; DOI=10.1016/s0167-4838(99)00122-3;
RA   Brannigan J.A., Ashford S.R., Doherty A.J., Timson D.J., Wigley D.B.;
RT   "Nucleotide sequence, heterologous expression and novel purification of DNA
RT   ligase from Bacillus stearothermophilus.";
RL   Biochim. Biophys. Acta 1432:413-418(1999).
RN   [2]
RP   X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-318, AND ACTIVE SITE.
RX   PubMed=10368271; DOI=10.1016/s0969-2126(99)80007-0;
RA   Singleton M.R., Hakansson K., Timson D.J., Wigley D.B.;
RT   "Structure of the adenylation domain of an NAD+-dependent DNA ligase.";
RL   Structure 7:35-42(1999).
CC   -!- FUNCTION: DNA ligase that catalyzes the formation of phosphodiester
CC       linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-
CC       stranded DNA using NAD as a coenzyme and as the energy source for the
CC       reaction. It is essential for DNA replication and repair of damaged
CC       DNA. {ECO:0000255|HAMAP-Rule:MF_01588}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-
CC         nicotinamide D-nucleotide.; EC=6.5.1.2; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01588};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC   -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC       subfamily. {ECO:0000255|HAMAP-Rule:MF_01588}.
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DR   EMBL; AJ011676; CAA09732.1; -; Genomic_DNA.
DR   RefSeq; WP_033016671.1; NZ_RCTK01000024.1.
DR   PDB; 1B04; X-ray; 2.80 A; A/B=1-318.
DR   PDBsum; 1B04; -.
DR   AlphaFoldDB; O87703; -.
DR   SMR; O87703; -.
DR   GeneID; 58573740; -.
DR   BRENDA; 6.5.1.2; 623.
DR   EvolutionaryTrace; O87703; -.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003911; F:DNA ligase (NAD+) activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   CDD; cd00114; LIGANc; 1.
DR   Gene3D; 2.40.50.140; -; 1.
DR   Gene3D; 3.40.50.10190; -; 1.
DR   HAMAP; MF_01588; DNA_ligase_A; 1.
DR   InterPro; IPR001357; BRCT_dom.
DR   InterPro; IPR036420; BRCT_dom_sf.
DR   InterPro; IPR041663; DisA/LigA_HHH.
DR   InterPro; IPR018239; DNA_ligase_AS.
DR   InterPro; IPR033136; DNA_ligase_CS.
DR   InterPro; IPR001679; DNAligase.
DR   InterPro; IPR013839; DNAligase_adenylation.
DR   InterPro; IPR013840; DNAligase_N.
DR   InterPro; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR004150; NAD_DNA_ligase_OB.
DR   InterPro; IPR010994; RuvA_2-like.
DR   InterPro; IPR004149; Znf_DNAligase_C4.
DR   Pfam; PF00533; BRCT; 1.
DR   Pfam; PF01653; DNA_ligase_aden; 1.
DR   Pfam; PF03120; DNA_ligase_OB; 1.
DR   Pfam; PF03119; DNA_ligase_ZBD; 1.
DR   Pfam; PF12826; HHH_2; 1.
DR   PIRSF; PIRSF001604; LigA; 1.
DR   SMART; SM00292; BRCT; 1.
DR   SMART; SM00278; HhH1; 3.
DR   SMART; SM00532; LIGANc; 1.
DR   SUPFAM; SSF47781; SSF47781; 1.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   SUPFAM; SSF52113; SSF52113; 1.
DR   TIGRFAMs; TIGR00575; dnlj; 1.
DR   PROSITE; PS50172; BRCT; 1.
DR   PROSITE; PS01055; DNA_LIGASE_N1; 1.
DR   PROSITE; PS01056; DNA_LIGASE_N2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA damage; DNA repair; DNA replication; Ligase; Magnesium;
KW   Manganese; Metal-binding; NAD; Zinc.
FT   CHAIN           1..670
FT                   /note="DNA ligase"
FT                   /id="PRO_0000161737"
FT   DOMAIN          589..670
FT                   /note="BRCT"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   ACT_SITE        114
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT                   ECO:0000305|PubMed:10368271"
FT   BINDING         34..38
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         83..84
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         112
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         135
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         169
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         285
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         309
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         403
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         406
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         421
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         426
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   HELIX           3..25
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           35..50
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           52..54
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           60..63
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           92..104
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          109..125
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          128..134
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          141..143
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           145..149
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          164..171
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           174..186
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           195..204
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           208..213
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          217..223
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   TURN            224..230
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           234..243
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          253..257
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           258..271
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          279..286
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   HELIX           289..295
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          299..301
FT                   /evidence="ECO:0007829|PDB:1B04"
FT   STRAND          305..309
FT                   /evidence="ECO:0007829|PDB:1B04"
SQ   SEQUENCE   670 AA;  74231 MW;  B52462314CF9ACF5 CRC64;
     MDRQQAERRA AELRELLNRY GYEYYVLDRP SVPDAEYDRL MQELIAIEEQ YPELKTSDSP
     TQRIGGPPLE AFRKVAHRVP MMSLANAFGE GDLRDFDRRV RQEVGEAAYV CELKIDGLAV
     SVRYEDGYFV QGATRGDGTT GEDITENLKT IRSLPLRLKE PVSLEARGEA FMPKASFLRL
     NEERKARGEE LFANPRNAAA GSLRQLDPKV AASRQLDLFV YGLADAEALG IASHSEALDY
     LQALGFKVNP ERRRCANIDE VIAFVSEWHD KRPQLPYEID GIVIKVDSFA QQRALGATAK
     SPRWAIAYKF PAEEVVTTLI GIEVNVGRTG VVTPTAILEP VRVAGTTVQR ATLHNEDFIR
     EKDIRIGDAV IIKKAGDIIP EVVGVVVDRR DGDETPFAMP THCPECESEL VRLEGEVALR
     CLNPNCPAQL RERLIHFASR AAMNIEGLGE KVVTQLFNAG LVRDVADLYC LTKEQLVGLE
     RMGEKSAANL LAAIEASKQN SLERLLFGLG IRYVGAKAAQ LLAEHFETME RLERATKEEL
     MAVPEIGEKM ADAITAFFAQ PEATELLQEL RAYGVNMAYK GPKRSAEAPA DSAFAGKTVV
     LTGKLASMSR NEAKEQIERL GGRVTGSVSR STDLVIAGED AGSKLEKAQQ LGIEIWDESR
     FLQEINRGKR
 
 
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