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DNLJ_HELPY
ID   DNLJ_HELPY              Reviewed;         656 AA.
AC   O25336;
DT   15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   03-AUG-2022, entry version 135.
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;
GN   OrderedLocusNames=HP_0615;
OS   Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC   Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC   Helicobacteraceae; Helicobacter.
OX   NCBI_TaxID=85962;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700392 / 26695;
RX   PubMed=9252185; DOI=10.1038/41483;
RA   Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA   Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA   Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA   Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA   McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA   Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA   Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA   Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT   "The complete genome sequence of the gastric pathogen Helicobacter
RT   pylori.";
RL   Nature 388:539-547(1997).
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; AE000511; AAD07680.1; -; Genomic_DNA.
DR   PIR; G64596; G64596.
DR   RefSeq; NP_207410.1; NC_000915.1.
DR   RefSeq; WP_000597558.1; NC_018939.1.
DR   PDB; 5FRQ; X-ray; 2.90 A; G/L=554-561.
DR   PDBsum; 5FRQ; -.
DR   AlphaFoldDB; O25336; -.
DR   SMR; O25336; -.
DR   DIP; DIP-3062N; -.
DR   IntAct; O25336; 5.
DR   MINT; O25336; -.
DR   STRING; 85962.C694_03180; -.
DR   PaxDb; O25336; -.
DR   EnsemblBacteria; AAD07680; AAD07680; HP_0615.
DR   KEGG; hpy:HP_0615; -.
DR   PATRIC; fig|85962.47.peg.663; -.
DR   eggNOG; COG0272; Bacteria.
DR   OMA; HDVEHEI; -.
DR   PhylomeDB; O25336; -.
DR   Proteomes; UP000000429; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003911; F:DNA ligase (NAD+) activity; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006288; P:base-excision repair, DNA ligation; IBA:GO_Central.
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; 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   Pfam; PF00533; BRCT; 1.
DR   Pfam; PF01653; DNA_ligase_aden; 1.
DR   Pfam; PF03120; DNA_ligase_OB; 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; Reference proteome; Zinc.
FT   CHAIN           1..656
FT                   /note="DNA ligase"
FT                   /id="PRO_0000161747"
FT   DOMAIN          577..656
FT                   /note="BRCT"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   ACT_SITE        112
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         32..36
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         81..82
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         133
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         167
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         306
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         400
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
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         416
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"
SQ   SEQUENCE   656 AA;  73900 MW;  A844F21C10057174 CRC64;
     MIKSQKEYLE RIAYLNTLSH HYYNLDEPIV SDAIYDELYQ ELKAYEEKNP NGIQANSPTQ
     KVGATTTNSF NKNPHLMRMW SLDDVFNQSE LQAWLQRILK AYPSASFVCS PKLDGVSLNL
     LYQHGKLVKA TTRGNGLEGE LVSANAKHIA NIPHAIAYNG EIEIRGEVII SKKDFDALNQ
     ERLNANEPLF ANPRNAASGS LRQLDSEITK KRKLQFIPWG VGKHSLNFLS FKECLDFIVS
     LGFSAIQYLS LNKNHQEIED NYHTLIRERE GFFALLDGMV IVVNELNIQK ELGYTQKSPK
     FACAYKFPAL EKHTKIVGVI NQVGRSGAIT PVALLEPVEI AGAMINRATL HNYSEIEKKN
     IMLSDRVVVI RSGDVIPKII KPLESYRDGS QHKIERPKVC PICSHELLCE EIFTYCQNLN
     CPARLKESLI HFASKDALNI QGLGDKVIEQ LFEEKLIFNA LDLYALKLED LMRLDKFKIK
     KAQNLLDAIL KSKNPPLWRL INALGIEHIG KGASKTLAKY GLNVLEKSEA EFLEMEGFGV
     EMARSLVNFY ASNQEFIRSL FELLNPKNSD MAEEKQKSSS VFNNKTIVLT GTLSKPRQEY
     AQMLENLGAK ISSSVSAKTD FLIAGENPGS KLALAQKHGV SVLNEEELLK RLKELD
 
 
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