DNLJ_NITWN
ID DNLJ_NITWN Reviewed; 716 AA.
AC Q3STR7;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2005, 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=Nwi_1062;
OS Nitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 /
OS NCIMB 11846 / Nb-255).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Nitrobacter.
OX NCBI_TaxID=323098;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255;
RX PubMed=16517654; DOI=10.1128/aem.72.3.2050-2063.2006;
RA Starkenburg S.R., Chain P.S.G., Sayavedra-Soto L.A., Hauser L., Land M.L.,
RA Larimer F.W., Malfatti S.A., Klotz M.G., Bottomley P.J., Arp D.J.,
RA Hickey W.J.;
RT "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium
RT Nitrobacter winogradskyi Nb-255.";
RL Appl. Environ. Microbiol. 72:2050-2063(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; CP000115; ABA04324.1; -; Genomic_DNA.
DR RefSeq; WP_011314358.1; NC_007406.1.
DR AlphaFoldDB; Q3STR7; -.
DR SMR; Q3STR7; -.
DR STRING; 323098.Nwi_1062; -.
DR PRIDE; Q3STR7; -.
DR EnsemblBacteria; ABA04324; ABA04324; Nwi_1062.
DR KEGG; nwi:Nwi_1062; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_5; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000002531; Chromosome.
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; 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; 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..716
FT /note="DNA ligase"
FT /id="PRO_0000313337"
FT DOMAIN 638..716
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 132
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 47..51
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 96..97
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 130
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 153
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 190
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 330
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
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 438
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 453
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 459
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 716 AA; 78589 MW; 0AFC83DB828C9665 CRC64;
MAAKSKTPPP VDSLTRSQAR VEHKRLALEI ETHNERYYQQ DAPTVSDATY DALQRRLEAI
EARFPDLVTA SSPTQTVGAA PARGFAKVQH AVPMLSLGNA FSDAEVAEFV ERIRRFLKLG
ADDMPAIVAE PKIDGLSLSL RYENGDLVRA ATRGDGFTGE DVTANVRTIA DVPHKLNGHN
IPTACELRGE VYMLKEDFLA LNKKQQEAGD TVFANPRNSA AGSLRQKDVS ITASRPLKFF
AYAWGEMTDR PAETQNDMLE WLRDVGFIVN PLIQLCHSVD EVLAFYRRIG EQRATLGYDI
DGVVYKVDRL DWQERLGFVS RSPRWAIAHK FAAEQAMTIL RGIDIQVGRT GAMTPVARLE
PVTVGGVVVQ NATLHNEDYI RGLGNDGQPI RDGIDLRIGD TVVVQRAGDV IPQVVSVIIE
KRPANAKRYE FPDRCPICGS HAVREEGEAV RRCTGALICP AQAVERLKHF VSRLAFDIDG
LGEKQIQEFY DDGLVMHPVD IFTLQERDAR AENKLRDRDG YGDVSVRNLF AAIDARRRIE
LNRLIFALGI RHVGEGNAKL LARHYGSIES FRSAMTEAAA AQTEAGNDSE AYADLTNIGG
IGDIVADAVV EFFAEPRNVK ALNDLLEEIE VLPVAQARSD SAVAGKTVVF TGSLEKFTRD
EAKASAERVG AKTSSSVSKK TDLVVAGPGA GSKLKDAEKF GVKVISEDEW LKLIEG
