DNLJ_XANAC
ID DNLJ_XANAC Reviewed; 833 AA.
AC Q8PM07;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 125.
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=XAC1627;
OS Xanthomonas axonopodis pv. citri (strain 306).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xanthomonas.
OX NCBI_TaxID=190486;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=306;
RX PubMed=12024217; DOI=10.1038/417459a;
RA da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R.,
RA Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr.,
RA Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G.,
RA Cannavan F., Cardozo J., Chambergo F., Ciapina L.P., Cicarelli R.M.B.,
RA Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B.,
RA Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F.,
RA Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T.,
RA Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A.,
RA Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J.,
RA Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M.,
RA Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A.,
RA Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A.,
RA Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M.,
RA Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P.;
RT "Comparison of the genomes of two Xanthomonas pathogens with differing host
RT specificities.";
RL Nature 417:459-463(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; AE008923; AAM36495.1; -; Genomic_DNA.
DR RefSeq; WP_011051040.1; NC_003919.1.
DR AlphaFoldDB; Q8PM07; -.
DR SMR; Q8PM07; -.
DR STRING; 190486.XAC1627; -.
DR EnsemblBacteria; AAM36495; AAM36495; XAC1627.
DR GeneID; 66910787; -.
DR KEGG; xac:XAC1627; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_6; -.
DR OMA; HDVEHEI; -.
DR Proteomes; UP000000576; 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; 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..833
FT /note="DNA ligase"
FT /id="PRO_0000313514"
FT DOMAIN 750..833
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 117
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 35..39
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 84..85
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 115
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 138
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 292
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 316
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 410
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 413
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 428
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 434
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 833 AA; 90484 MW; 3666A2B3B6A2243D CRC64;
MTASPDPAQR IDALRRRIED ANYRYHVLDE PQMADADYDK LMRELEALER AHPELASADS
PTQRVGHLAA SRFAEVRHAM PMLSLGNAFS DEEVTEFVRR ISERLEVRQP LFSAEPKLDG
LAISLRYENG EFVQGATRGD GATGEDVSAN LRTVKAIPLR LRGEGWPRVL EVRGEVYMPR
AAFEAYNAQM RAQGGKILAN PRNGAAGSLR QLDARITAQR PLSFFAYGVG EVSEGALPQA
HSAILAQLRA WGFPVSALVE VVQGSDGLLA YYQRIGEARD GLAFDIDGVV YKLDDLAGQR
EMGFVSRAPR WAIAHKFPAQ EQSTTVEAIE IQIGRTGAAT PVARLKPVHV AGVIVTNATL
HNADQIARLD VRVGDTVIVR RAGDVIPEVA AVVADQRPPG TQAWQMPTQC PVCGSEIVRE
EGQAVWRCSG ELTCPAQRKE AFRHFVSRRA MDVDGLGEKF IEVLVDSGLV KGVADLYLLS
VDQLLQLRLI STADSPHAFL REAREHLASG AYAQLEASVV GIGVDLAGER DVPQTWQADL
LRAGLPSFDW NRKKIATKWA ENLIEAIEIS RDTTLERFLF ALGIEHVGES TAKALSAWFG
DLELIRHLPW PLFKRVPDIG GEVARSLGHF FDQAGNQKAI DHLLARKVRI GDTHPPSPKL
RGELSLANLL EDLEIPKVTP IRAAQIATAF GSIDALRNGG PEPLVEAGVP QSVAESLAAW
LLVPANDTLA VNAQRKLSEL LAMLPEAGEE KTGPLDGQTV VITGTLAALT RDAAKQRLEA
LGAKVAGSVS KKTAFLVAGE EAGSKLDKAQ SLGVEIWDEA RLLAFLGDHG QQP
