ID   Q5WHL9_SHOC1            Unreviewed;       602 AA.
AC   Q5WHL9;
DT   23-NOV-2004, integrated into UniProtKB/TrEMBL.
DT   23-NOV-2004, sequence version 1.
DT   27-MAR-2024, entry version 96.
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=ABC1601 {ECO:0000313|EMBL:BAD64136.1};
OS   Shouchella clausii (strain KSM-K16) (Alkalihalobacillus clausii).
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Shouchella.
OX   NCBI_TaxID=66692 {ECO:0000313|EMBL:BAD64136.1, ECO:0000313|Proteomes:UP000001168};
RN   [1] {ECO:0000313|EMBL:BAD64136.1, ECO:0000313|Proteomes:UP000001168}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KSM-K16 {ECO:0000313|EMBL:BAD64136.1,
RC   ECO:0000313|Proteomes:UP000001168};
RA   Hakamada Y., Kobayashi T., Hitomi J., Kawai S., Ito S.;
RT   "Molecular cloning and nucleotide sequence of the gene for an alkaline
RT   protease from the alkalophilic Bacillus sp. KSM-K16.";
RL   J. Ferment. Bioeng. 78:105-108(1994).
RN   [2] {ECO:0000313|EMBL:BAD64136.1, ECO:0000313|Proteomes:UP000001168}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KSM-K16 {ECO:0000313|EMBL:BAD64136.1,
RC   ECO:0000313|Proteomes:UP000001168};
RX   PubMed=7632397; DOI=10.1007/s002530050437;
RA   Kobayashi T., Hakamada Y., Adachi S., Hitomi J., Yoshimatsu T., Koike K.,
RA   Kawai S., Ito S.;
RT   "Purification and properties of an alkaline protease from alkalophilic
RT   Bacillus sp. KSM-K16.";
RL   Appl. Microbiol. Biotechnol. 43:473-481(1995).
RN   [3] {ECO:0000313|EMBL:BAD64136.1, ECO:0000313|Proteomes:UP000001168}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KSM-K16 {ECO:0000313|EMBL:BAD64136.1,
RC   ECO:0000313|Proteomes:UP000001168};
RX   PubMed=9278275; DOI=10.1093/protein/10.6.627;
RA   Shirai T., Suzuki A., Yamane T., Ashida T., Kobayashi T., Ito S.;
RT   "High-resolution crystal structure of M-protease: phylogeny aided analysis
RT   of the high-alkaline adaptation mechanism.";
RL   Protein Eng. 10:627-634(1997).
RN   [4] {ECO:0000313|Proteomes:UP000001168}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KSM-K16 {ECO:0000313|Proteomes:UP000001168};
RA   Takaki Y., Kageyama Y., Shimamura S., Suzuki H., Nishi S., Hatada Y.,
RA   Kawai S., Ito S., Horikoshi K.;
RT   "The complete genome sequence of the alkaliphilic Bacillus clausii KSM-
RT   K16.";
RL   Submitted (OCT-2003) to the EMBL/GenBank/DDBJ databases.
RN   [5] {ECO:0000313|EMBL:BAD64136.1, ECO:0000313|Proteomes:UP000001168}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=KSM-K16 {ECO:0000313|EMBL:BAD64136.1,
RC   ECO:0000313|Proteomes:UP000001168};
RX   PubMed=17429572; DOI=10.1007/s00792-007-0074-1;
RA   Kageyama Y., Takaki Y., Shimamura S., Nishi S., Nogi Y., Uchimura K.,
RA   Kobayashi T., Hitomi J., Ozaki K., Kawai S., Ito S., Horikoshi K.;
RT   "Intragenomic diversity of the V1 regions of 16S rRNA genes in high-
RT   alkaline protease-producing Bacillus clausii spp.";
RL   Extremophiles 11:597-603(2007).
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; AP006627; BAD64136.1; -; Genomic_DNA.
DR   RefSeq; WP_011246445.1; NC_006582.1.
DR   AlphaFoldDB; Q5WHL9; -.
DR   STRING; 66692.ABC1601; -.
DR   KEGG; bcl:ABC1601; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_2_9; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000001168; 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; cd04866; LigD_Pol_like_3; 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   InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR   InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR   InterPro; IPR014146; LigD_ligase_dom.
DR   InterPro; IPR033652; LigD_Pol-like_3.
DR   InterPro; IPR014145; LigD_pol_dom.
DR   InterPro; IPR014143; NHEJ_ligase_prk.
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; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF21686; LigD_Prim-Pol; 1.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   PROSITE; PS00333; DNA_LIGASE_A2; 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};
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:UP000001168};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          125..230
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
SQ   SEQUENCE   602 AA;  69019 MW;  FCEE90B0F7028B29 CRC64;
     MKPMKLTETT AFPQSTGWVA EPKYDGYRCL VSITDTSIEL ISRNGRLLNH AFPEVVSAFE
     ERRTKLSNEL PLVLDGELVC LLNGYASHFP AVQTRSRMSN VHVIEKEMVS RPCQWIAFDI
     LNQPNVPYRE RRKQLLSFCK RADIPALTPL GGVPTLGVVE STSAIQALLT TVKRYNGEGI
     VLKKQLSPYN QNIRSKDWLK LKHYRLVPVL VTFFDATNGY FHGSVYHQQG ALNEVAIFKH
     GLLPDDAKTL ANFFRTKGTA EKNGFRLAPS IVVELACIGL SGGQLREVSF VRFLHHADPN
     DITMTTLFHG LYPLPDIVET TSLDKPLWEQ VTKADYLHYL QAVMPFMLPF LYQRALTVIR
     FPHGTFANER FYQKHIPNYA PAYVNSAWLE DICYILCNNP ETLIWLGNQL ALELHIPFQT
     IESSKPDEIV FDLDPPSQDQ FGLAQEAALD MKQIFNRFQL PFFCKTTGGK GLQVHIPLEK
     QTLTYEETGR FMKFVADFLC QQKPGKYTTE RLKKKRRNRL YIDYVQHAYN KTVIAPYSMR
     ETGFAAVPLR EDELASPTLS PQQFSYVDVL RRIQQFENPF IGYERERVSK ERFIQLLDEI
     GI
//