DNLJ_GEMAT
ID DNLJ_GEMAT Reviewed; 689 AA.
AC C1A6H2;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 1.
DT 03-AUG-2022, entry version 68.
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=GAU_0790;
OS Gemmatimonas aurantiaca (strain T-27 / DSM 14586 / JCM 11422 / NBRC
OS 100505).
OC Bacteria; Gemmatimonadetes; Gemmatimonadales; Gemmatimonadaceae;
OC Gemmatimonas.
OX NCBI_TaxID=379066;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=T-27 / DSM 14586 / JCM 11422 / NBRC 100505;
RA Takasaki K., Ichikawa N., Miura H., Matsushita S., Watanabe Y., Oguchi A.,
RA Ankai A., Yashiro I., Takahashi M., Terui Y., Fukui S., Yokoyama H.,
RA Tanikawa S., Hanada S., Kamagata Y., Fujita N.;
RT "Complete genome sequence of Gemmatimonas aurantiaca T-27 that represents a
RT novel phylum Gemmatimonadetes.";
RL Submitted (MAR-2006) 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: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; AP009153; BAH37832.1; -; Genomic_DNA.
DR RefSeq; WP_012682279.1; NC_012489.1.
DR AlphaFoldDB; C1A6H2; -.
DR SMR; C1A6H2; -.
DR STRING; 379066.GAU_0790; -.
DR EnsemblBacteria; BAH37832; BAH37832; GAU_0790.
DR KEGG; gau:GAU_0790; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_0; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000002209; 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; 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; 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 Pfam; PF00533; BRCT; 1.
DR Pfam; PF01653; DNA_ligase_aden; 1.
DR Pfam; PF03120; DNA_ligase_OB; 1.
DR Pfam; PF12826; HHH_2; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00278; HhH1; 3.
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..689
FT /note="DNA ligase"
FT /id="PRO_0000380387"
FT DOMAIN 600..689
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 124
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 40..44
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 89..90
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 122
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 145
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 182
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 300
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 325
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 419
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 422
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 437
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 442
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 689 AA; 74174 MW; 55B6927E11591FA1 CRC64;
MTASSGTPPH QTVERARELR EQLGTAQHEY YVLDRPTLSD QEYDRLFREL QGIEAEYPTL
CTEDSPTRRV GAPVQSAFSP HRHLVRMLSL DNAFDLSELE DFEQSLKRVV GDAIHTSGYT
VELKIDGAAV ALTYREGVLV TAATRGDGTD GEDVTANVRT IRGVPLRLHG DNHPPLMEVR
GEVYLPFAGF ERMNEARVAA GEPVYVNPRN AAAGSMRQLD SANTAARPLR FFGYAAVLPD
GSAPARSQWE LLEQLSAWGV PVAPHRQRCH TIQEAEAWAT VVEHETRATL GFAIDGGVVK
VNDMALQDEL GIRADRTPRW GVARKFAPDM ALTKLRRIDV NVGRTGVLTP FAVLEPVDVG
GATVTFASLH NADQIAAKDL REGDTVQVVR AGDVIPYVLG PVPEQRDGSQ QPWSMPTQCP
RCNTPVERYG DDVAVYCPNV ACPGRQLEGL VHFSSKDALD IDGLSYARIQ QLLDAGLVHD
VADLFDITVD QLTSLERFAK KSAENLVAAI AAAKQQPLSR LMFGLGIRHV GAQAAQLLSR
QYGSLDALMN ATAEQLGAVR GIGSIIAQSV ASYFADPTTR ALMERLRARG LRFDEPNAVQ
ADGVLTGATV VLTGTLPSLS RGEATALVEQ AGGRVTSSVS KKTTFVVAGE EAGSKLDKAK
ELGVTVLTEA ELLEKLSGAS ADASADASA
