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DNLJ_HELP2
ID   DNLJ_HELP2              Reviewed;         656 AA.
AC   B6JLJ9;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   16-DEC-2008, sequence version 1.
DT   03-AUG-2022, entry version 76.
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}; OrderedLocusNames=HPP12_0624;
OS   Helicobacter pylori (strain P12).
OC   Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC   Helicobacteraceae; Helicobacter.
OX   NCBI_TaxID=570508;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=P12;
RA   Fischer W., Windhager L., Karnholz A., Zeiller M., Zimmer R., Haas R.;
RT   "The complete genome sequence of Helicobacter pylori strain P12.";
RL   Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases.
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; CP001217; ACJ07777.1; -; Genomic_DNA.
DR   RefSeq; WP_000597671.1; NC_011498.1.
DR   AlphaFoldDB; B6JLJ9; -.
DR   SMR; B6JLJ9; -.
DR   EnsemblBacteria; ACJ07777; ACJ07777; HPP12_0624.
DR   KEGG; hpp:HPP12_0624; -.
DR   HOGENOM; CLU_007764_2_1_7; -.
DR   OMA; HDVEHEI; -.
DR   OrthoDB; 241401at2; -.
DR   Proteomes; UP000008198; Chromosome.
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; 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   3: Inferred from homology;
KW   DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW   Metal-binding; NAD; Zinc.
FT   CHAIN           1..656
FT                   /note="DNA ligase"
FT                   /id="PRO_0000380396"
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;  74051 MW;  9FF4622DA666F228 CRC64;
     MIKSQKEYLE RIEYLNTLSH HYYNLDESIV SDAVYDELYQ ELKAYEEKNP NDIQANSPTQ
     KVGATTTTPF SKNPHLMRMW SLDDVFNQSE LQAWLQRILK VYPNASFVCS PKLDGVSLNL
     LYHHGKLVSA TTRGNGLEGE LVTNNAKHIA NIPHFIAYDG EIEIRGEVII SKEDFEALNK
     ERLEANEPLF ANPRNAASGS LRQLDSEITK KRKLQFIPWG VGKHSLNFLS FKECLDFIVS
     LGFGAIQYLS LNKNHQEIEE SYHTLIKERE GFFALLDGMV IVVNELGIQK ELGYTQKSPK
     FACAYKFPAL EKHTKIIGVI NQVGRSGAIT PVALLEPVEI AGAMVNRATL HNYSEIEKKN
     IMLNDRVVVI RSGDVIPKII KPLETYRDGS QHKIERPKVC PICSHELLCE EIFTYCQNLN
     CPARLKESLI HFASKDALNI QGLGDKVIEQ LFEEKLIVNA LDLYALKLED LMRLDKFKIK
     KAQNLLDAIQ KSKNPPLWRL INALGIEHIG KGASKTLARY GLNVLEKSEA EFLEMEGFGV
     EMAHSLVNFY ASNQEFIRSL FDLLNPKNSD MAKEKQKSSS VFNNKTIVLT GTLSKPRQEY
     AQMLENLGAK ISSSVSAKTD FLIVGENPGS KLALAKKHGV SVLNEEELLK RLKELD
 
 
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