DNLJ_DESHY
ID DNLJ_DESHY Reviewed; 659 AA.
AC Q24QL5;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 18-APR-2006, sequence version 1.
DT 03-AUG-2022, entry version 98.
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=DSY3888;
OS Desulfitobacterium hafniense (strain Y51).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Desulfitobacteriaceae;
OC Desulfitobacterium.
OX NCBI_TaxID=138119;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Y51;
RX PubMed=16513756; DOI=10.1128/jb.188.6.2262-2274.2006;
RA Nonaka H., Keresztes G., Shinoda Y., Ikenaga Y., Abe M., Naito K.,
RA Inatomi K., Furukawa K., Inui M., Yukawa H.;
RT "Complete genome sequence of the dehalorespiring bacterium
RT Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides
RT ethenogenes 195.";
RL J. Bacteriol. 188:2262-2274(2006).
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; AP008230; BAE85677.1; -; Genomic_DNA.
DR RefSeq; WP_005812372.1; NC_007907.1.
DR AlphaFoldDB; Q24QL5; -.
DR SMR; Q24QL5; -.
DR STRING; 138119.DSY3888; -.
DR EnsemblBacteria; BAE85677; BAE85677; DSY3888.
DR KEGG; dsy:DSY3888; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_9; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000001946; 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 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; 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..659
FT /note="DNA ligase"
FT /id="PRO_0000313216"
FT DOMAIN 582..659
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 110
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 168
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 284
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 308
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 402
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 405
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 420
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 425
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 659 AA; 72979 MW; B107856AD0061CF2 CRC64;
MPDVSQRIEA LREQIEEANY QYYGLDQPTL SDAEYDALLQ ELIRLEKEHP EFLTPDSPSQ
RVGGYIAKEF PKVRHAEALL SLDNAFDAGD LLEFDRRVRA LVAEVEYVVE LKIDGLTVAL
TYEDGALVRG ATRGDGEVGE EITANLKTIP AIPLRLRKQA DRLDVRGEGY MPKGSFLRLN
QEREEAGQPL FANPRNAAAG SLRQLDSRIT AQRKLGYFAY QVLTPEEGEL ASQTAVLDYL
KEQGFSVNPE YRVFSAIEEV IAYCGEMVEK RHNYPYDIDG LVIKVNDIAQ QRELGFTAKS
PRWAIAYKFP AEQVETVVED IVIRVGRTGV LTPTAYLTPV FVAGSTVGRA TLHNLDNIRA
KDVRIGDHVL IQKAGDVIPE VVKILPEKRT GGERIFEMPE LCPECQSPVI REEGEAAHRC
TSITCPARQR EAIIHFVSRN AMNIDGLGPA VIYQLLEAGL IKDAADLYAL EYDALVPLER
LGKKSAENLL KAIEDSKERG LAPLIFGLGI RHVGEKAGKI LAQKYGTMED LEKAQVEELQ
EIPDVGPAMA QSVAQFFQQE STHHFLNKLR QAGVVMSAQH SAKPQIFAGK SIVVTGSLQR
WDRHYVETMI EEFGGKAASS VSKKTAFVVA GEKAGSKLAK AKELGIPVLS EEEFAELLP
