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DNLJ_AGRVS
ID   DNLJ_AGRVS              Reviewed;         719 AA.
AC   B9JY41;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   24-MAR-2009, sequence version 1.
DT   03-AUG-2022, entry version 77.
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=Avi_2876;
OS   Agrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain
OS   S4)).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
OX   NCBI_TaxID=311402;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=S4 / ATCC BAA-846;
RX   PubMed=19251847; DOI=10.1128/jb.01779-08;
RA   Slater S.C., Goldman B.S., Goodner B., Setubal J.C., Farrand S.K.,
RA   Nester E.W., Burr T.J., Banta L., Dickerman A.W., Paulsen I., Otten L.,
RA   Suen G., Welch R., Almeida N.F., Arnold F., Burton O.T., Du Z., Ewing A.,
RA   Godsy E., Heisel S., Houmiel K.L., Jhaveri J., Lu J., Miller N.M.,
RA   Norton S., Chen Q., Phoolcharoen W., Ohlin V., Ondrusek D., Pride N.,
RA   Stricklin S.L., Sun J., Wheeler C., Wilson L., Zhu H., Wood D.W.;
RT   "Genome sequences of three Agrobacterium biovars help elucidate the
RT   evolution of multichromosome genomes in bacteria.";
RL   J. Bacteriol. 191:2501-2511(2009).
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; CP000633; ACM37071.1; -; Genomic_DNA.
DR   RefSeq; WP_015916492.1; NC_011989.1.
DR   AlphaFoldDB; B9JY41; -.
DR   SMR; B9JY41; -.
DR   STRING; 311402.Avi_2876; -.
DR   EnsemblBacteria; ACM37071; ACM37071; Avi_2876.
DR   KEGG; avi:Avi_2876; -.
DR   eggNOG; COG0272; Bacteria.
DR   HOGENOM; CLU_007764_2_1_5; -.
DR   OMA; HDVEHEI; -.
DR   OrthoDB; 241401at2; -.
DR   Proteomes; UP000001596; Chromosome 1.
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   3: Inferred from homology;
KW   DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW   Metal-binding; NAD; Reference proteome; Zinc.
FT   CHAIN           1..719
FT                   /note="DNA ligase"
FT                   /id="PRO_0000380284"
FT   DOMAIN          641..719
FT                   /note="BRCT"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   ACT_SITE        129
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         44..48
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         93..94
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         127
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         150
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         186
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         302
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         326
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         432
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         435
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         456
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         462
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   719 AA;  78786 MW;  9650DE67831D74B4 CRC64;
     MADALIPVED LSEEQAGQEL IRLAAAIAHH DALYHGKDQP EISDADYDAL KRRNDAIEAR
     FPTLVRSDSP SQRVGAAPAG IFSQITHARP MLSLDNTFSD EDVADFVASV YRFLGVMPDN
     SIAFTAEPKI DGLSMSIRYE HRKLKTAATR GDGTTGENVT ANILTIKEIP TELPADAPDV
     VEVRGEVYMA KSDFLALNAQ MEAEGRQTYV NPRNTAAGSL RQLDAKVTAS RKLKFFAYAW
     GEMSTMPAET QSGMVEAFKR WGFPVNPLTR RLTSVEEIIA HYREIGLQRA DLDYDIDGVV
     YKVDRLDLQA RLGFRSRSPR WATAHKFPAE QAFTTVEAID IQVGRTGALT PVARLEPITV
     GGVVVTNATL HNADYIEGIG NGGERIRPEG HDIRIGDTVI VQRAGDVIPQ VLDVVLEKRP
     ETSVKYEFPK TCPVCGSHAV REKNEKTGKL DSVTRCTGGF VCSAQAKEHI KHFVSRNAFD
     IEGLGTKQVD FFFESEDPAL MIRTAPDIFT LKQRQEASSL TRLENIDGFG RVSVRKLFDA
     IDARREIALN RFIFALGIRH VGETTAKLLA RSYGSYAAFA DAMQEAAPKF GEAWNELNSI
     DGIGEVVAAS MVEFFKEPRN LEVVSRLLKE VTPLDAEAVT ASDSPVAGKT VVFTGSLERF
     TRDEAKARAE SLGAKVAGSV SKKTDYLVAG PGAGSKLDKA REVGVTVMTE DEWLALIGW
 
 
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