ID H3R8V4_PANSE Unreviewed; 672 AA.
AC H3R8V4;
DT 18-APR-2012, integrated into UniProtKB/TrEMBL.
DT 18-APR-2012, sequence version 1.
DT 24-JAN-2024, entry version 65.
DE RecName: Full=DNA ligase {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE EC=6.5.1.2 {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000256|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000256|HAMAP-Rule:MF_01588,
GN ECO:0000313|EMBL:EHU01617.1};
GN ORFNames=CKS_0044 {ECO:0000313|EMBL:EHU01617.1}, DSJ_18320
GN {ECO:0000313|EMBL:ARF51076.1};
OS Pantoea stewartii subsp. stewartii DC283.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Erwiniaceae; Pantoea.
OX NCBI_TaxID=660596 {ECO:0000313|EMBL:EHU01617.1, ECO:0000313|Proteomes:UP000005050};
RN [1] {ECO:0000313|EMBL:EHU01617.1, ECO:0000313|Proteomes:UP000005050}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DC283 {ECO:0000313|EMBL:EHU01617.1,
RC ECO:0000313|Proteomes:UP000005050};
RX PubMed=22111898; DOI=10.1111/j.1365-2958.2011.07926.x;
RA Wang X., Yang F., von Bodman S.B.;
RT "The genetic and structural basis of two distinct terminal side branch
RT residues in stewartan and amylovoran exopolysaccharides and their potential
RT role in host adaptation.";
RL Mol. Microbiol. 83:195-207(2012).
RN [2] {ECO:0000313|EMBL:EHU01617.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=DC283 {ECO:0000313|EMBL:EHU01617.1};
RA Biehl B.S., Ding Y., Dugan-Rocha S.P., Gibbs R.A., Glasner J.D., Kovar C.,
RA Muzny D.M., Neeno-Eckwall E.C., Perna N.T., Qin X., von Bodman S.B.,
RA Weinstock G.M.;
RL Submitted (JAN-2012) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:ARF51076.1, ECO:0000313|Proteomes:UP000192380}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DC283 {ECO:0000313|EMBL:ARF51076.1,
RC ECO:0000313|Proteomes:UP000192380};
RA Duong D.A., Stevens A.M., Jensen R.V.;
RT "Complete Genome Assembly of Pantoea stewartii subsp. stewartii DC283, a
RT Corn Pathogen.";
RL Submitted (OCT-2016) 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:0000256|ARBA:ARBA00004067, ECO:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00034005, ECO:0000256|HAMAP-
CC Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC subfamily. {ECO:0000256|HAMAP-Rule:MF_01588}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01588}.
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DR EMBL; CP017581; ARF51076.1; -; Genomic_DNA.
DR EMBL; AHIE01000002; EHU01617.1; -; Genomic_DNA.
DR RefSeq; WP_006117795.1; NZ_CP017581.1.
DR AlphaFoldDB; H3R8V4; -.
DR STRING; 660596.DSJ_18320; -.
DR KEGG; pstw:DSJ_18320; -.
DR PATRIC; fig|660596.6.peg.280; -.
DR eggNOG; COG0272; Bacteria.
DR OrthoDB; 9759736at2; -.
DR Proteomes; UP000005050; Unassembled WGS sequence.
DR Proteomes; UP000192380; 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; cd17748; BRCT_DNA_ligase_like; 1.
DR CDD; cd00114; LIGANc; 1.
DR Gene3D; 6.20.10.30; -; 1.
DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 2.
DR Gene3D; 3.40.50.10190; BRCT domain; 1.
DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR Gene3D; 1.10.287.610; Helix hairpin bin; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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; IPR001679; DNA_ligase.
DR InterPro; IPR018239; DNA_ligase_AS.
DR InterPro; IPR033136; DNA_ligase_CS.
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 NCBIfam; TIGR00575; dnlj; 1.
DR PANTHER; PTHR23389; CHROMOSOME TRANSMISSION FIDELITY FACTOR 18; 1.
DR PANTHER; PTHR23389:SF9; DNA LIGASE; 1.
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 Pfam; PF14520; HHH_5; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00278; HhH1; 4.
DR SMART; SM00532; LIGANc; 1.
DR SUPFAM; SSF52113; BRCT domain; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR SUPFAM; SSF47781; RuvA domain 2-like; 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 {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_01588};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01588};
KW Manganese {ECO:0000256|HAMAP-Rule:MF_01588};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01588};
KW NAD {ECO:0000256|ARBA:ARBA00023027, ECO:0000256|HAMAP-Rule:MF_01588};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT DOMAIN 594..672
FT /note="BRCT"
FT /evidence="ECO:0000259|PROSITE:PS50172"
FT ACT_SITE 115
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 32..36
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 81..82
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 113
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 136
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 173
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 290
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 314
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 408
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 411
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 432
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ SEQUENCE 672 AA; 74176 MW; 2D49B3933722D835 CRC64;
MKSVQEHITE LRTTLRHHEY LYHVMDAPEV PDAEYDRLMR ELRDLEAQHP DLITPDSPTQ
RVGAAPLMVF EQVRHEVPML SLDNAFDEAS FRAFNKRVQD RLKSTDDLTY CCELKLDGLA
VSLLYEDGLL TRAATRGDGT TGENITTNVR TIRAIPLRLK GDNIPARVEV RGEVFMTQSG
FEKLNAEARR TEGKVFANPR NAAAGSLRQL DPRITAKRPL TFFCYGLGLL EGGEMPRSHM
ARLQQFKAWG LPVSDRIRLV QNADEALAFY HEVESERATL GFDIDGVVIK VDSQELQEKL
GFVARAPRWA VAFKFPAQEQ MTIVCDVEFQ VGRTGAITPV ARLEPVQVAG VMVSNATLHN
ADEIERLGLR IGDKVVIRRA GDVIPQVVNV VTSERPDNAR EIVFPSQCPV CGSDVERVEG
EAVTRCTGGL ICGAQRKEAL KHFVSRRAMD VDGMGDKIID QLVEKEYVKT PADLFRLSRE
TLTGLDRMGA KSAQNVVDAL EKAKSTTLAR FLYALGIREV GEATAANLAS HFGDLQKVMD
ADLDALIAVQ DVGTVVAKHV RHFMEEESNR EVIRQLVEDI GIHWPQVVAV NPGEIDSPFA
GKTVVLTGSL SQMNRDDAKA RLIELGAKVS GSVSKKTDLL IAGEAAGSKL AKAQELGIEI
IDEAEMIRRL GA
//
