GenomeNet

Database: UniProt
Entry: O34398
LinkDB: O34398
Original site: O34398 
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   07-JUN-2017, entry version 100.
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; Firmicutes; 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.,
RA   Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S.,
RA   Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S.,
RA   Brouillet S., Bruschi C.V., Caldwell B., Capuano V., Carter N.M.,
RA   Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A.,
RA   Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T.,
RA   Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D.,
RA   Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N.,
RA   Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G.,
RA   Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A.,
RA   Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M.,
RA   Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M.,
RA   Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S.,
RA   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.,
RA   Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B.,
RA   Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R.,
RA   Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P.,
RA   Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H.,
RA   Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P.,
RA   Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F.,
RA   Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H.,
RA   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.,
RA   Devine K.M., Bowater R.P., Jeggo P.A., Jackson S.P., Doherty A.J.;
RT   "Identification of a DNA nonhomologous end-joining complex in
RT   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
RT   spore resistance to extreme dryness, mono- and polychromatic UV, and
RT   ionizing radiation.";
RL   J. Bacteriol. 189:3306-3311(2007).
CC   -!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) DNA
CC       repair enzyme, which repairs dsDNA breaks with reduced fidelity
CC       (Probable). Probably involved in DNA repair during spore
CC       germination. {ECO:0000305}.
CC   -!- FUNCTION: The preference of the polymerase domain for rNTPs over
CC       dNTPs may be advantageous in dormant cells, where the dNTP pool
CC       may be limiting. {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
CC       5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
CC       AMP + diphosphate.
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
CC       1 for ligase activity. {ECO:0000250};
CC   -!- SUBUNIT: Interacts with Ku. {ECO:0000250}.
CC   -!- INDUCTION: Transcriptionally regulated by SpoVT and sigma-G
CC       factor. {ECO:0000269|PubMed:16497325}.
CC   -!- DISRUPTION PHENOTYPE: Stationary-phase cells lacking this gene are
CC       more sensitive to ionizing radiation (IR) than cells lacking Ku
CC       (YkoV); a double mutant is not more sensitive than the ku
CC       knockout. Spores lacking this gene are more sensitive to UV, IR,
CC       ultrahigh vacuum, and dry heat. {ECO:0000269|PubMed:12215643,
CC       ECO:0000269|PubMed:16497325, ECO:0000269|PubMed:17293412}.
CC   -!- MISCELLANEOUS: LigD has variable architecture. In Bacillus lacks
CC       the 3'-phosphoesterase domain (PE) found in Mycobacteria and some
CC       Gammaproteobacteria.
CC   -!- SIMILARITY: In the N-terminal section; belongs to the LigD
CC       polymerase family. {ECO:0000305}.
CC   -!- SIMILARITY: In the C-terminal section; belongs to the ATP-
CC       dependent DNA ligase family. {ECO:0000305}.
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   ProteinModelPortal; O34398; -.
DR   SMR; O34398; -.
DR   STRING; 224308.Bsubs1_010100007426; -.
DR   PaxDb; O34398; -.
DR   PRIDE; O34398; -.
DR   EnsemblBacteria; CAB13197; CAB13197; BSU13400.
DR   GeneID; 939372; -.
DR   KEGG; bsu:BSU13400; -.
DR   PATRIC; fig|224308.179.peg.1455; -.
DR   eggNOG; ENOG4105DQE; Bacteria.
DR   eggNOG; COG1793; LUCA.
DR   eggNOG; COG3285; LUCA.
DR   HOGENOM; HOG000008893; -.
DR   InParanoid; O34398; -.
DR   KO; K01971; -.
DR   OMA; AMMVEDH; -.
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; cd04866; LigD_Pol_like_3; 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   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   TIGRFAMs; TIGR02778; ligD_pol; 1.
DR   TIGRFAMs; TIGR02779; NHEJ_ligase_lig; 1.
DR   TIGRFAMs; TIGR02776; NHEJ_ligase_prk; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   2: Evidence at transcript level;
KW   ATP-binding; Complete proteome; DNA damage; DNA recombination;
KW   DNA repair; DNA-binding; DNA-directed DNA polymerase; Exonuclease;
KW   Hydrolase; Ligase; Manganese; Metal-binding; Multifunctional enzyme;
KW   Nuclease; Nucleotide-binding; Nucleotidyltransferase;
KW   Reference proteome; Sporulation; Transferase.
FT   CHAIN         1    611       Bifunctional non-homologous end joining
FT                                protein LigD.
FT                                /FTId=PRO_0000389505.
FT   REGION        5    310       Ligase domain (Lig).
FT   REGION      325    564       DNA repair polymerase domain (Pol).
FT   ACT_SITE     24     24       N6-AMP-lysine intermediate.
FT                                {ECO:0000250}.
FT   METAL        26     26       Manganese 1. {ECO:0000250}.
FT   METAL       184    184       Manganese 1. {ECO:0000250}.
FT   METAL       439    439       Manganese 2. {ECO:0000250}.
FT   METAL       439    439       Manganese 3. {ECO:0000250}.
FT   METAL       441    441       Manganese 2. {ECO:0000250}.
FT   METAL       441    441       Manganese 3. {ECO:0000250}.
FT   METAL       530    530       Manganese 3. {ECO:0000250}.
FT   BINDING      22     22       ATP. {ECO:0000250}.
FT   BINDING      29     29       ATP. {ECO:0000250}.
FT   BINDING      44     44       ATP. {ECO:0000250}.
FT   BINDING      78     78       ATP. {ECO:0000250}.
FT   BINDING     119    119       ATP. {ECO:0000250}.
FT   BINDING     200    200       ATP. {ECO:0000250}.
FT   BINDING     206    206       ATP. {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
//
DBGET integrated database retrieval system