DNLJ_CLOBJ
ID DNLJ_CLOBJ Reviewed; 664 AA.
AC C1FLS8;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 1.
DT 03-AUG-2022, entry version 70.
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=CLM_3704;
OS Clostridium botulinum (strain Kyoto / Type A2).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Clostridiaceae;
OC Clostridium.
OX NCBI_TaxID=536232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Kyoto / Type A2;
RA Shrivastava S., Brinkac L.M., Brown J.L., Bruce D., Detter C.C.,
RA Johnson E.A., Munk C.A., Smith L.A., Smith T.J., Sutton G., Brettin T.S.;
RT "Genome sequence of Clostridium botulinum A2 Kyoto.";
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; CP001581; ACO84729.1; -; Genomic_DNA.
DR RefSeq; WP_012704383.1; NC_012563.1.
DR AlphaFoldDB; C1FLS8; -.
DR SMR; C1FLS8; -.
DR STRING; 536232.CLM_3704; -.
DR EnsemblBacteria; ACO84729; ACO84729; CLM_3704.
DR KEGG; cby:CLM_3704; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_9; -.
DR OMA; HDVEHEI; -.
DR Proteomes; UP000001374; 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; IPR041663; DisA/LigA_HHH.
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 Pfam; PF12826; HHH_2; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00278; HhH1; 4.
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; 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..664
FT /note="DNA ligase"
FT /id="PRO_0000380342"
FT DOMAIN 587..664
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 122
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 80..81
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 144
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 178
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 314
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 407
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 410
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 423
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 429
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 664 AA; 75804 MW; 4AA03F3FE074C6AF CRC64;
MDNKLEKMKE LVEELNQYAY EYYVLDNPSI SDKEYDLKYD ELVILEKKTE VTLPYSPTQR
VGDKILGEFS KYTHKGRLWS LDKAQNMEQL IEWHNRNLKV IEQYNSMSED KLPELRYIVT
KKFDGLTVNC TYDENGILIK SATRGTGIIG EDITAQIKTI KTVPLKIKNN HVIEVHGEAI
MTKTAFEEYN KAAQVPLKNL RNGAAGALRN LDIKETARRN LSAFFYDVGY NEGPEFKSYR
EMMNFIKNMG LPQDKYIKEC TNMEEVEKEI EYIESIRGEL DYDIDGAVIV VDDIKTREIL
GYTIKFPKWA IAYKFEAKEI TTKLLDVEWN VGRSGRVTPT ALLEPVELGG VTVKRATLNN
MDDIKRKNVK LGAKVLVRRS NDVIPEIMGV VEESLEESEE IQAPDRCPYC NSHLVQNGVH
YYCENTLSCK PQMVKSIVHF ASREAMNIAG FSEKTAEQLF EKLDIKSIAD LYKIKKEELL
TLEKFKDKKS QNLIDAIQNS KNCDLASFIY ALGIPNVGKK TANDLVMKFK TLESIKNTTI
EQLVEVPDVG EIVAKSIYDF FEDEKIISNI EELLNLGVKP YYEEERIDEN PFMGKTIVVT
GSLNNYSRGE IKDKLQSLGA KVSSSVSKNT DYVLVGEKPG SKYEKAIELG VKVINEEEFS
NKIK
