DNLJ_BRADU
ID DNLJ_BRADU Reviewed; 716 AA.
AC Q89FV8;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 115.
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=bll6591;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
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; BA000040; BAC51856.1; -; Genomic_DNA.
DR RefSeq; NP_773231.1; NC_004463.1.
DR AlphaFoldDB; Q89FV8; -.
DR SMR; Q89FV8; -.
DR STRING; 224911.27354871; -.
DR EnsemblBacteria; BAC51856; BAC51856; BAC51856.
DR KEGG; bja:bll6591; -.
DR PATRIC; fig|224911.5.peg.6748; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_0_5; -.
DR InParanoid; Q89FV8; -.
DR OMA; GRDQLDI; -.
DR PhylomeDB; Q89FV8; -.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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; IPR041663; DisA/LigA_HHH.
DR InterPro; IPR018239; DNA_ligase_AS.
DR InterPro; IPR001679; DNAligase.
DR InterPro; IPR013839; DNAligase_adenylation.
DR InterPro; IPR013840; DNAligase_N.
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; 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.
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..716
FT /note="DNA ligase"
FT /id="PRO_0000313149"
FT DOMAIN 638..716
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 134
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 50..54
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 99..100
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 132
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 155
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 192
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 332
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 437
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 439
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 461
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 467
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 716 AA; 79565 MW; E31CDDC5B2928161 CRC64;
MMARAAKSKP LRDVAELTKA QAKVELMRLA LELEGHDKRY YQDDAPTVTD AEYDALRQRF
NAIEKRFPEF VSAESPSQKV GAAPSGRFRK VRHAVPMLSL DNAFAEEDVR DFVGRIVRFL
KLDDDKIDFS AEPKIDGLSM SLRYEGGELV TAATRGDGAE GEDVTANIRT LEDVPQKLKG
RNVPDICEVR GEVYMTKKAF LALNERQKAA GDTIFANPRN SAAGSLRQKD PTITASRPLG
FFAYAWGEMS AMPEETQTGM IHWFERCGFK TNPLTRLCHS VEELIAFHQR IEEERAELDY
DIDGVVYKVD RIDWQERLGF VSRTPRWGIA HKFPAEQAMT VLRDIEIQVG RTGSFTPVGK
LEPVGVGGVI VQNVTLHNED YIKGIGNKGE VLREGRDIRI GDTVVIQRAG DVIPQVVDVV
LDKRPKTAKE FHFPKTCPCP LHTDVTREET AAGEEGSRAR CTGEFACPYQ KIEHLKLFVS
RRAFDIDGLG EKQLQYFFDE GFVKEPADIF TLEKRNAKLK LEEIEGYGAT SVRNLFAAIE
SRRRIALERF VYALGMRHVG ETTALALARG YGSWEAFHDA CLKVAKGDEE AMADMDALDQ
IGDTVIKSIA DYFGESHNRG IVERLTKEVE IVDAEKPKSN SAVAGKTVVF TGSLEKMTRD
EAKATAERLG AKVSGSVSKK TDLVVAGPGA GSKLAEANKH GVKVLTEDEW LKLIGE
