ID A0A3N4VFP3_9GAMM Unreviewed; 784 AA.
AC A0A3N4VFP3;
DT 13-FEB-2019, integrated into UniProtKB/TrEMBL.
DT 13-FEB-2019, sequence version 1.
DT 24-JAN-2024, entry version 20.
DE RecName: Full=DNA ligase {ECO:0000256|HAMAP-Rule:MF_01588};
DE EC=6.5.1.2 {ECO:0000256|HAMAP-Rule:MF_01588};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000256|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000256|HAMAP-Rule:MF_01588};
GN ORFNames=EDC50_0689 {ECO:0000313|EMBL:RPE81498.1};
OS Vulcaniibacterium tengchongense.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Vulcaniibacterium.
OX NCBI_TaxID=1273429 {ECO:0000313|EMBL:RPE81498.1, ECO:0000313|Proteomes:UP000269708};
RN [1] {ECO:0000313|EMBL:RPE81498.1, ECO:0000313|Proteomes:UP000269708}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 25623 {ECO:0000313|EMBL:RPE81498.1,
RC ECO:0000313|Proteomes:UP000269708};
RA Goeker M.;
RT "Genomic Encyclopedia of Type Strains, Phase IV (KMG-IV): sequencing the
RT most valuable type-strain genomes for metagenomic binning, comparative
RT biology and taxonomic classification.";
RL Submitted (NOV-2018) 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|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};
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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:RPE81498.1}.
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DR EMBL; RKQN01000001; RPE81498.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A3N4VFP3; -.
DR OrthoDB; 9759736at2; -.
DR Proteomes; UP000269708; Unassembled WGS sequence.
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; 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 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 PIRSF; PIRSF001604; LigA; 2.
DR SMART; SM00292; BRCT; 1.
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; 2.
DR PROSITE; PS50172; BRCT; 1.
DR PROSITE; PS01055; DNA_LIGASE_N1; 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 Reference proteome {ECO:0000313|Proteomes:UP000269708};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT DOMAIN 698..764
FT /note="BRCT"
FT /evidence="ECO:0000259|PROSITE:PS50172"
FT ACT_SITE 113
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 31..35
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 80..81
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 111
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 134
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 171
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 288
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 312
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 406
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 409
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 430
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ SEQUENCE 784 AA; 85622 MW; 0F39489D44725C06 CRC64;
MPVDARIADL RRQLDEANYR YYVLDDPTIP DAEYDRLLRE LEALEAAHPE LASPDSPTQR
VGNAPSGAFA EVRHAVPMLS LANAFTDEEV ADFVRRIDER LGRDQLAFSV EPKLDGLAIS
LRYEDGRFVR GATRGDGATG EDVTANLRTI KAVPLRLRGR DWPRTLEVRG EVYMPVAAFR
AYNERALAEG RKPLANPRNG AAGSLRQLDP RVTAQRPLAF YAYGVGAFEG GELPPTHSRT
LAKLREWGFP VSAENRVVDG LDGLLGYYRE IGAKRERLPF EIDGVVYKLD DYAGQREMGF
VSRAPRWAIA HKFPAQEQAT VVESIEVNVG RTGAVTPWAL MQPVQVGGVT VTRATLHNAD
QVARLDVRNG DTVIVRRAGD VIPEVVRVVP ERRPPGTTPW RMPTHCPVCG SELVREEDAA
VWRCSGELVC PAQRKEAIIH FASRRAMDID GLGERYIEDL SDLGYVASVA DLYKLTLDDL
LEMKRRADER DGTVPETVKA GKVATKWAEN LIGAIDRSRR TTLERFLNAL GIQHVGESTA
KALAAWYGDI EVIRRLPWPL FKRVPDVGGE VARAIGHFFG QAGNQEVIDR LLERGVVITD
VHPPQPKLRE GLDFATLLVD LEIPKITRVR AEQLAAAFPD GTGLVEAEEH RFVAAGLPAD
TAQALAAWLR EPAHAQLLRQ GLDALARLDA VTPALEAAPS GPLDGRTAVL TGTLASMGRD
EAKARLEALG AKVAGSVSKK TSFVVAGEAA GSKLDKAQEL GVEIWDEARL LAFLAEHGAA
PGGA
//
