DNLJ_TREPA
ID DNLJ_TREPA Reviewed; 823 AA.
AC O83642;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 138.
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}; Synonyms=lig;
GN OrderedLocusNames=TP_0634;
OS Treponema pallidum (strain Nichols).
OC Bacteria; Spirochaetes; Spirochaetales; Treponemataceae; Treponema.
OX NCBI_TaxID=243276;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Nichols;
RX PubMed=9665876; DOI=10.1126/science.281.5375.375;
RA Fraser C.M., Norris S.J., Weinstock G.M., White O., Sutton G.G.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Clayton R.A., Ketchum K.A.,
RA Sodergren E., Hardham J.M., McLeod M.P., Salzberg S.L., Peterson J.D.,
RA Khalak H.G., Richardson D.L., Howell J.K., Chidambaram M., Utterback T.R.,
RA McDonald L.A., Artiach P., Bowman C., Cotton M.D., Fujii C., Garland S.A.,
RA Hatch B., Horst K., Roberts K.M., Sandusky M., Weidman J.F., Smith H.O.,
RA Venter J.C.;
RT "Complete genome sequence of Treponema pallidum, the syphilis spirochete.";
RL Science 281:375-388(1998).
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; AE000520; AAC65609.1; -; Genomic_DNA.
DR PIR; H71300; H71300.
DR RefSeq; WP_010882080.1; NC_021490.2.
DR AlphaFoldDB; O83642; -.
DR SMR; O83642; -.
DR IntAct; O83642; 15.
DR STRING; 243276.TPANIC_0634; -.
DR EnsemblBacteria; AAC65609; AAC65609; TP_0634.
DR GeneID; 57879157; -.
DR KEGG; tpa:TP_0634; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_3_12; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000000811; 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; -; 3.
DR HAMAP; MF_01588; DNA_ligase_A; 1.
DR InterPro; IPR001357; BRCT_dom.
DR InterPro; IPR036420; BRCT_dom_sf.
DR InterPro; IPR018239; DNA_ligase_AS.
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; 3.
DR Pfam; PF01653; DNA_ligase_aden; 1.
DR Pfam; PF03120; DNA_ligase_OB; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 3.
DR SMART; SM00278; HhH1; 2.
DR SMART; SM00532; LIGANc; 1.
DR SUPFAM; SSF47781; SSF47781; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 3.
DR TIGRFAMs; TIGR00575; dnlj; 1.
DR PROSITE; PS50172; BRCT; 3.
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; Reference proteome; Repeat; Zinc.
FT CHAIN 1..823
FT /note="DNA ligase"
FT /id="PRO_0000161774"
FT DOMAIN 562..655
FT /note="BRCT 1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT DOMAIN 654..742
FT /note="BRCT 2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT DOMAIN 741..823
FT /note="BRCT 3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 100
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 31..35
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 73..74
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 121
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 163
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 275
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 296
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 387
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 390
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 403
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 408
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 823 AA; 91098 MW; 1EFC9DBC57532A6B CRC64;
MSTAQRRVQE LEKLILHHQD RYYNAESDIS DDAFDALWEE LARLDPGNPL LKAIGSDSQR
DAVKKRHIVP MGSQHKAADE ESFSAWAKKN ALQAFLVQHK LDGVSLELQY ERGHFCCALT
RGNGIVGDDV TANVRGMRGF VPTLTAEWGP CGNLPFTGGV RGEVIMHKDI HRSHYPTHAN
CRNTVNGILK RKDGRGRTHL HIVCYDAVPG TPGKPFTGSL PFADETEKLA WLARQGFVTV
HSHRCANAQE VVALRSEIMR TRELLPYSID GLVVKSTDLD FQDAQLPRPK KQIAFKFSTQ
EAITTLRDVQ WQTSGVTYTP IGITDPVRLA GTTVKRANLC NPNMLTKLCL KIGSHVLISK
RGEIIPKIEA LVSTPAHAQE IHIPTQCTSC NTVLENSGSR LFCPNVNCPL LSHHRITRWI
ECLEIKHVGT ELIQRLFEEK KVRRIPDLYT LTCEDLIEIE HVGNATAKKI LEAIHHKKEI
ALQTFIAGFG IEGIGETMGE KLICAGFDTL EKVLHATTET LESIYQFGTE LAKSVVTGIA
RVKDDMCELL DRGFVRILAK QQAESPLRGK SFCFSGSLRN GDRATIHRIR ALGGVVRTSV
TRDLSYLIFE SLSQPYRTAQ KLKKEQGVAL EIISEDEFCR LLDQASASCT HTGETVHPLQ
GKSFYFSGAS RSMNHKHAQE KVRALGGDVA SSVTAQLDYL VFYSQSTRYR TACALGIQII
SEETLHKLIA TAQSPLHTDA HVHAPLHGMS FCFSGDLDGM TRAQAIALVQ RLGGTVKTAV
STQLTYLVSN DPHGQSRKCQ NAVRCGVRII SEHVFLALCT PGT
