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Database: UniProt/SWISS-PROT
Entry: LIGD_BACSU
LinkDB: LIGD_BACSU
Original site: LIGD_BACSU 
ID   LIGD_BACSU              Reviewed;         611 AA.
AC   O34398;
DT   24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   24-JAN-2024, entry version 117.
DE   RecName: Full=Bifunctional non-homologous end joining protein LigD;
DE   AltName: Full=NHEJ DNA polymerase;
DE   Includes:
DE     RecName: Full=DNA ligase;
DE              Short=Lig;
DE              EC=6.5.1.1;
DE     AltName: Full=Polydeoxyribonucleotide synthase [ATP];
DE   Includes:
DE     RecName: Full=DNA repair polymerase;
DE              Short=Pol;
DE     AltName: Full=Polymerase/primase;
GN   Name=ligd; Synonyms=ykoU; OrderedLocusNames=BSU13400;
OS   Bacillus subtilis (strain 168).
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=224308;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=9384377; DOI=10.1038/36786;
RA   Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA   Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA   Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA   Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA   Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA   Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA   Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA   Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA   Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA   Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA   Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA   Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA   Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA   Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA   Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA   Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA   Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA   Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA   Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA   Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA   Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA   Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA   Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA   Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA   Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA   Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA   Yoshikawa H., Danchin A.;
RT   "The complete genome sequence of the Gram-positive bacterium Bacillus
RT   subtilis.";
RL   Nature 390:249-256(1997).
RN   [2]
RP   PROBABLE FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=168;
RX   PubMed=12215643; DOI=10.1126/science.1074584;
RA   Weller G.R., Kysela B., Roy R., Tonkin L.M., Scanlan E., Della M.,
RA   Devine S.K., Day J.P., Wilkinson A., d'Adda di Fagagna F., Devine K.M.,
RA   Bowater R.P., Jeggo P.A., Jackson S.P., Doherty A.J.;
RT   "Identification of a DNA nonhomologous end-joining complex in bacteria.";
RL   Science 297:1686-1689(2002).
RN   [3]
RP   PROBABLE FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=168 / PY79;
RX   PubMed=16497325; DOI=10.1016/j.jmb.2006.01.059;
RA   Wang S.T., Setlow B., Conlon E.M., Lyon J.L., Imamura D., Sato T.,
RA   Setlow P., Losick R., Eichenberger P.;
RT   "The forespore line of gene expression in Bacillus subtilis.";
RL   J. Mol. Biol. 358:16-37(2006).
RN   [4]
RP   PROBABLE FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=168;
RX   PubMed=17293412; DOI=10.1128/jb.00018-07;
RA   Moeller R., Stackebrandt E., Reitz G., Berger T., Rettberg P.,
RA   Doherty A.J., Horneck G., Nicholson W.L.;
RT   "Role of DNA repair by nonhomologous-end joining in Bacillus subtilis spore
RT   resistance to extreme dryness, mono- and polychromatic UV, and ionizing
RT   radiation.";
RL   J. Bacteriol. 189:3306-3311(2007).
CC   -!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) DNA repair
CC       enzyme, which repairs dsDNA breaks with reduced fidelity (Probable).
CC       Probably involved in DNA repair during spore germination.
CC       {ECO:0000305}.
CC   -!- FUNCTION: The preference of the polymerase domain for rNTPs over dNTPs
CC       may be advantageous in dormant cells, where the dNTP pool may be
CC       limiting. {ECO:0000250}.
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;
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Binds 3 Mn(2+); 2 Mn(2+) for polymerase/primase activity and 1 for
CC       ligase activity. {ECO:0000250};
CC   -!- SUBUNIT: Interacts with Ku. {ECO:0000250}.
CC   -!- INDUCTION: Transcriptionally regulated by SpoVT and sigma-G factor.
CC       {ECO:0000269|PubMed:16497325}.
CC   -!- DISRUPTION PHENOTYPE: Stationary-phase cells lacking this gene are more
CC       sensitive to ionizing radiation (IR) than cells lacking Ku (YkoV); a
CC       double mutant is not more sensitive than the ku knockout. Spores
CC       lacking this gene are more sensitive to UV, IR, ultrahigh vacuum, and
CC       dry heat. {ECO:0000269|PubMed:12215643, ECO:0000269|PubMed:16497325,
CC       ECO:0000269|PubMed:17293412}.
CC   -!- MISCELLANEOUS: LigD has variable architecture. In Bacillus lacks the
CC       3'-phosphoesterase domain (PE) found in Mycobacteria and some
CC       Gammaproteobacteria.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the LigD polymerase
CC       family. {ECO:0000305}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the ATP-dependent DNA
CC       ligase family. {ECO:0000305}.
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DR   EMBL; AL009126; CAB13197.1; -; Genomic_DNA.
DR   PIR; G69860; G69860.
DR   RefSeq; NP_389223.1; NC_000964.3.
DR   RefSeq; WP_010886495.1; NZ_JNCM01000035.1.
DR   AlphaFoldDB; O34398; -.
DR   SMR; O34398; -.
DR   STRING; 224308.BSU13400; -.
DR   PaxDb; 224308-BSU13400; -.
DR   EnsemblBacteria; CAB13197; CAB13197; BSU_13400.
DR   GeneID; 939372; -.
DR   KEGG; bsu:BSU13400; -.
DR   PATRIC; fig|224308.179.peg.1455; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   InParanoid; O34398; -.
DR   OMA; YMANLGC; -.
DR   OrthoDB; 9802472at2; -.
DR   PhylomeDB; O34398; -.
DR   BioCyc; BSUB:BSU13400-MONOMER; -.
DR   Proteomes; UP000001570; 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   GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; 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; 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; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING 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; PS50160; DNA_LIGASE_A3; 1.
PE   2: Evidence at transcript level;
KW   ATP-binding; DNA damage; DNA recombination; DNA repair; DNA-binding;
KW   DNA-directed DNA polymerase; Exonuclease; Hydrolase; Ligase; Manganese;
KW   Metal-binding; Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW   Nucleotidyltransferase; Reference proteome; Sporulation; Transferase.
FT   CHAIN           1..611
FT                   /note="Bifunctional non-homologous end joining protein
FT                   LigD"
FT                   /id="PRO_0000389505"
FT   REGION          5..310
FT                   /note="Ligase domain (Lig)"
FT   REGION          325..564
FT                   /note="DNA repair polymerase domain (Pol)"
FT   ACT_SITE        24
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000250"
FT   BINDING         22
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         26
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         29
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         44
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         78
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         119
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         184
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         200
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         206
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         439
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         439
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         441
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         441
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
FT   BINDING         530
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   611 AA;  70204 MW;  5CB06797A2C955C0 CRC64;
     MAFTMQPVLT SSPPIGAEWR YEVKYDGYRC ILRIHSSGVT LTSRNGVELS STFPEITQFA
     KTAFQHLEKE LPLTLDGEIV CLVNPCRADF EHLQVRGRLK RPDKIQESAN ARPCCFLAFD
     LLERSGEDVT LLSYLDRKKS LRELISAAKL PASPDPYAKE TIQSIPCYDH FDQLWEMVIK
     YDGEGIVAKK TNSKWLEKKR SSDWLKYKNF KQAYVCITGF NPNNGFLTVS VLKNGIMTPI
     ASVSHGMRDE EKSAIREIME QHGHQTPSGE FTLEPSICAA VQYLTILQGT LREVSFIGFE
     FQMDWTECTY AQVIRHSKPV HPKLQFTSLD KIIFEKNKKT KEDFIQYMIE VSDYLLPFLK
     NRAVTVIRYP HGSRSESFFQ KNKPDYAPDF VQSFYDGSHE HIVCEDMSTL LWLCNQLALE
     FHVPFQTIKS RRPAEIVIDL DPPSRDDFLM AVQAANELKR LLDSFGITSY PKLSGNKGIQ
     LYIPLSPEAF TYEETRQFTQ LIAEYCTNAF PELFTTERLI KNRHCKLYLD YLQHAEGKTI
     ICPYSTRGNE LGTVAAPLYW HEVQSSLTPA LFTIDTVIDR IKKQGCPFFD FYRNPQDEPL
     SAILHQLKKK S
//
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