DNLJ_XYLFM
ID DNLJ_XYLFM Reviewed; 831 AA.
AC B0U5G7;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 28-JUL-2009, sequence version 2.
DT 03-AUG-2022, entry version 81.
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};
GN OrderedLocusNames=Xfasm12_2128;
OS Xylella fastidiosa (strain M12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xylella.
OX NCBI_TaxID=405440;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=M12;
RX PubMed=20601474; DOI=10.1128/jb.00651-10;
RA Chen J., Xie G., Han S., Chertkov O., Sims D., Civerolo E.L.;
RT "Whole genome sequences of two Xylella fastidiosa strains (M12 and M23)
RT causing almond leaf scorch disease in California.";
RL J. Bacteriol. 192:4534-4534(2010).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ACA12985.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; CP000941; ACA12985.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_020851963.1; NC_010513.1.
DR AlphaFoldDB; B0U5G7; -.
DR SMR; B0U5G7; -.
DR KEGG; xfm:Xfasm12_2128; -.
DR HOGENOM; CLU_007764_2_2_6; -.
DR OrthoDB; 241401at2; -.
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; 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; 2.
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; Zinc.
FT CHAIN 1..831
FT /note="DNA ligase"
FT /id="PRO_0000380512"
FT DOMAIN 749..831
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 116
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 34..38
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 83..84
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 114
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 137
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 174
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 291
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 315
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 409
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 427
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 433
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 831 AA; 91654 MW; FA4CBEE3C30FD2C3 CRC64;
MIPLDPAQRA AELRRRLQEA NYHYHVLDQP RIPDADYDRM LRELDALEAT YPDLATPDSP
TQRVGHTIAT AFSEVRHTVP MLSLNNAFSD PEVLEFVRRI TARLGETAPS FSAEPKLDGL
AISLRYQNGI FIQGATRGDG VTGEDVTANL RTLPTIPQRL QSDTWPTVLE VRGEVYMPRP
DFEAYNTQAR LRGWKVLANP RNGAAGSLRQ LDPHITAQRP LSFYAYGIGE VADDVSFHSH
SEILASLRAW GFPVSPLVEL VYGSEGLLNY YRRMETIRDT LPFDIDGIVY KLDDLSGQHE
MGFVARAPRW AIAHKFPAQE QTTTVEAIEI QIGRTGAATP VARLTPVQVA GVTVTSATLH
NADQIARLDV RIGDTVIVRR AGDVIPEVVA VITDSRPPGV TAWSMPMACP VCGSEIVRET
GAAVWRCSGE LACPAQRKEA IRHFVSRRAM DVEGLGVKCI ELLVDAAVVH GVADLYHLSL
DQLLRLRLVT NAQTPTMLLR EARDHVTGMR YQQLEEILRT VGVDLSGEGD VPEHWQIDVL
RAQWPDFDWN HKKIATKWAQ NLIAAIDRSR QTTLERFLFA LGMTHVGETT AKALAHSFGD
LAIIRQLPWP LFKCVPDIGG EVARAIGHFM DQPANQQAID DLVERGVRIT DAHPPTSTLR
DQLTLASLLE HLEIPKITPM RAVQLATLAP TLPLLAEADL DALLQAGVPQ PAAQSLTEWF
QSPDNISLAR RLQHCCDVLL AQLPSPDRAH TAPLNGQSVV LTGKLASLTR EAAATRLEML
GAKIVGSVSK KTSFLVAGED PGSKLDKAHA LHVDIWDEAR LLDFLEQYSA Q
