ID   Q3SGP7_THIDA            Unreviewed;       846 AA.
AC   Q3SGP7;
DT   11-OCT-2005, integrated into UniProtKB/TrEMBL.
DT   11-OCT-2005, sequence version 1.
DT   27-MAR-2024, entry version 105.
DE   RecName: Full=DNA ligase (ATP) {ECO:0000256|ARBA:ARBA00012727};
DE            EC=6.5.1.1 {ECO:0000256|ARBA:ARBA00012727};
DE   AltName: Full=NHEJ DNA polymerase {ECO:0000256|ARBA:ARBA00029943};
GN   OrderedLocusNames=Tbd_2247 {ECO:0000313|EMBL:AAZ98200.1};
OS   Thiobacillus denitrificans (strain ATCC 25259).
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales;
OC   Thiobacillaceae; Thiobacillus.
OX   NCBI_TaxID=292415 {ECO:0000313|EMBL:AAZ98200.1, ECO:0000313|Proteomes:UP000008291};
RN   [1] {ECO:0000313|EMBL:AAZ98200.1, ECO:0000313|Proteomes:UP000008291}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25259 {ECO:0000313|EMBL:AAZ98200.1,
RC   ECO:0000313|Proteomes:UP000008291};
RX   PubMed=16452431; DOI=10.1128/JB.188.4.1473-1488.2006;
RA   Beller H.R., Chain P.S., Letain T.E., Chakicherla A., Larimer F.W.,
RA   Richardson P.M., Coleman M.A., Wood A.P., Kelly D.P.;
RT   "The genome sequence of the obligately chemolithoautotrophic, facultatively
RT   anaerobic bacterium Thiobacillus denitrificans.";
RL   J. Bacteriol. 188:1473-1488(2006).
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC         diphosphate.; EC=6.5.1.1; Evidence={ECO:0000256|ARBA:ARBA00034003};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|ARBA:ARBA00001936};
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DR   EMBL; CP000116; AAZ98200.1; -; Genomic_DNA.
DR   RefSeq; WP_011312759.1; NC_007404.1.
DR   AlphaFoldDB; Q3SGP7; -.
DR   STRING; 292415.Tbd_2247; -.
DR   KEGG; tbd:Tbd_2247; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_4; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000008291; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
DR   GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   CDD; cd07906; Adenylation_DNA_ligase_LigD_LigC; 1.
DR   CDD; cd07971; OBF_DNA_ligase_LigD; 1.
DR   CDD; cd04862; PaeLigD_Pol_like; 1.
DR   Gene3D; 3.30.1490.70; -; 1.
DR   Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR   Gene3D; 3.90.920.10; DNA primase, PRIM domain; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR   InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR   InterPro; IPR014146; LigD_ligase_dom.
DR   InterPro; IPR014144; LigD_PE_domain.
DR   InterPro; IPR014145; LigD_pol_dom.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR014143; NHEJ_ligase_prk.
DR   InterPro; IPR033651; PaeLigD_Pol-like.
DR   NCBIfam; TIGR02777; LigD_PE_dom; 1.
DR   NCBIfam; TIGR02778; ligD_pol; 1.
DR   NCBIfam; TIGR02779; NHEJ_ligase_lig; 1.
DR   NCBIfam; TIGR02776; NHEJ_ligase_prk; 1.
DR   PANTHER; PTHR42705; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING PROTEIN LIGD; 1.
DR   PANTHER; PTHR42705:SF2; MULTIFUNCTIONAL NON-HOMOLOGOUS END JOINING DNA REPAIR PROTEIN LIGD; 1.
DR   Pfam; PF04679; DNA_ligase_A_C; 1.
DR   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF13298; LigD_N; 1.
DR   Pfam; PF21686; LigD_Prim-Pol; 1.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   4: Predicted;
KW   ATP-binding {ECO:0000256|ARBA:ARBA00022840};
KW   DNA damage {ECO:0000256|ARBA:ARBA00022763};
KW   DNA recombination {ECO:0000256|ARBA:ARBA00023172};
KW   DNA repair {ECO:0000256|ARBA:ARBA00023204};
KW   DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW   DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932};
KW   Exonuclease {ECO:0000256|ARBA:ARBA00022839};
KW   Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000313|EMBL:AAZ98200.1};
KW   Manganese {ECO:0000256|ARBA:ARBA00023211};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW   Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW   Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW   Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW   Reference proteome {ECO:0000313|Proteomes:UP000008291};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          334..469
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          1..29
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          186..216
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        186..213
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   846 AA;  92492 MW;  66AE24D0BA3B1FAC CRC64;
     MAKRDPLSTY TEKRDFSISP EPVSGGQANE AARSFVVQKH WATRLHYDFR LELDGSMKSW
     AVPKGPSLDP ADKRMAVHVE DHPIAYNAFE GTIPPRQYGA GKVIIWDKGT WVPLVDPRRG
     YEEGHLKFEL HGHKLQGRWA LVRMKGKGEA KEPWLLIKEK DEHARPAADY SVVDALPDSV
     ADKDDAAAVT KAAAPRRRAG ETPRPRKARA AKATEKAGAA AVEGAVKSAL PATLAPQLAT
     LADKPPDDGD GWVYEVKFDG YRMLARIDKT VRLFTRNGND WSHRLAPLVK AIEAAGLRPG
     WLDGEVVVPN AAGVPDFQAL QNAFDQARAD AIVYYVFDLP FYDGYDLRAA PLVARKALLA
     GLLDTPHSDA LRLSESFDAA PRDILASACK MGLEGVIAKR RDAPYVSRRS TDWLKLKCTR
     RQEFVIGGYT DPRGSRPGLG SLLLGVHDAR GELVYAGNVG TGFDHGTLGD LRKKLAAHAR
     DTSPFVDATG IAGKPHWVDP KLVAEVSFGE WTKSGRIRHA VFEGLRLDKR AASVVREEPV
     AAAAAAPRLP ADLKVSHPER VVDKASGTTK LALIAYYARV APLMMPHLKA RPVSLVRAPD
     GVGGSLFFQK HVEASQMRGV KTLPRTLDPG HAPLIEVAAA EGLLTAAQMN VIEFHTWNAR
     KTRIDKPDRM TFDLDPGEGV GWTTVQESAH LVREFLSQLG LASFLKTSGG KGLHIVVPLK
     RLHDWDTVKD FSHAIVRHLA RTLPQRFAAK SGPKNRVGKI FIDYLRNGFG ATTVAAWSVR
     ARPGLGVSVP LEWRELDALT SAAQWTVPNI DSRLEIGNAP WEAYDASSHS LTRAMKTLGH
     VPKTPA
//