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Bifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP]); DNA repair polymerase (Pol) (Polymerase/primase)]

 LIGD_BACSU              Reviewed;         611 AA.
O34398;
24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
01-JAN-1998, sequence version 1.
07-JUN-2017, entry version 100.
RecName: Full=Bifunctional non-homologous end joining protein LigD;
AltName: Full=NHEJ DNA polymerase;
Includes:
RecName: Full=DNA ligase;
Short=Lig;
EC=6.5.1.1;
AltName: Full=Polydeoxyribonucleotide synthase [ATP];
Includes:
RecName: Full=DNA repair polymerase;
Short=Pol;
AltName: Full=Polymerase/primase;
Name=ligd; Synonyms=ykoU; OrderedLocusNames=BSU13400;
Bacillus subtilis (strain 168).
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
NCBI_TaxID=224308;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=168;
PubMed=9384377; DOI=10.1038/36786;
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G.,
Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S.,
Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S.,
Brouillet S., Bruschi C.V., Caldwell B., Capuano V., Carter N.M.,
Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A.,
Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T.,
Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D.,
Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N.,
Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G.,
Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A.,
Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M.,
Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M.,
Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S.,
Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G.,
Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B.,
Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R.,
Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P.,
Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H.,
Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P.,
Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F.,
Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H.,
Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
Yoshikawa H., Danchin A.;
"The complete genome sequence of the Gram-positive bacterium Bacillus
subtilis.";
Nature 390:249-256(1997).
[2]
PROBABLE FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=168;
PubMed=12215643; DOI=10.1126/science.1074584;
Weller G.R., Kysela B., Roy R., Tonkin L.M., Scanlan E., Della M.,
Devine S.K., Day J.P., Wilkinson A., d'Adda di Fagagna F.,
Devine K.M., Bowater R.P., Jeggo P.A., Jackson S.P., Doherty A.J.;
"Identification of a DNA nonhomologous end-joining complex in
bacteria.";
Science 297:1686-1689(2002).
[3]
PROBABLE FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
STRAIN=168 / PY79;
PubMed=16497325; DOI=10.1016/j.jmb.2006.01.059;
Wang S.T., Setlow B., Conlon E.M., Lyon J.L., Imamura D., Sato T.,
Setlow P., Losick R., Eichenberger P.;
"The forespore line of gene expression in Bacillus subtilis.";
J. Mol. Biol. 358:16-37(2006).
[4]
PROBABLE FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=168;
PubMed=17293412; DOI=10.1128/JB.00018-07;
Moeller R., Stackebrandt E., Reitz G., Berger T., Rettberg P.,
Doherty A.J., Horneck G., Nicholson W.L.;
"Role of DNA repair by nonhomologous-end joining in Bacillus subtilis
spore resistance to extreme dryness, mono- and polychromatic UV, and
ionizing radiation.";
J. Bacteriol. 189:3306-3311(2007).
-!- FUNCTION: With Ku forms a non-homologous end joining (NHEJ) DNA
repair enzyme, which repairs dsDNA breaks with reduced fidelity
(Probable). Probably involved in DNA repair during spore
germination. {ECO:0000305}.
-!- FUNCTION: The preference of the polymerase domain for rNTPs over
dNTPs may be advantageous in dormant cells, where the dNTP pool
may be limiting. {ECO:0000250}.
-!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
AMP + diphosphate.
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Binds 3 Mn(2+); 2 Mn(2+) for polymerase/primase activity and
1 for ligase activity. {ECO:0000250};
-!- SUBUNIT: Interacts with Ku. {ECO:0000250}.
-!- INDUCTION: Transcriptionally regulated by SpoVT and sigma-G
factor. {ECO:0000269|PubMed:16497325}.
-!- DISRUPTION PHENOTYPE: Stationary-phase cells lacking this gene are
more sensitive to ionizing radiation (IR) than cells lacking Ku
(YkoV); a double mutant is not more sensitive than the ku
knockout. Spores lacking this gene are more sensitive to UV, IR,
ultrahigh vacuum, and dry heat. {ECO:0000269|PubMed:12215643,
ECO:0000269|PubMed:16497325, ECO:0000269|PubMed:17293412}.
-!- MISCELLANEOUS: LigD has variable architecture. In Bacillus lacks
the 3'-phosphoesterase domain (PE) found in Mycobacteria and some
Gammaproteobacteria.
-!- SIMILARITY: In the N-terminal section; belongs to the LigD
polymerase family. {ECO:0000305}.
-!- SIMILARITY: In the C-terminal section; belongs to the ATP-
dependent DNA ligase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL009126; CAB13197.1; -; Genomic_DNA.
PIR; G69860; G69860.
RefSeq; NP_389223.1; NC_000964.3.
RefSeq; WP_010886495.1; NZ_JNCM01000035.1.
ProteinModelPortal; O34398; -.
SMR; O34398; -.
STRING; 224308.Bsubs1_010100007426; -.
PaxDb; O34398; -.
PRIDE; O34398; -.
EnsemblBacteria; CAB13197; CAB13197; BSU13400.
GeneID; 939372; -.
KEGG; bsu:BSU13400; -.
PATRIC; fig|224308.179.peg.1455; -.
eggNOG; ENOG4105DQE; Bacteria.
eggNOG; COG1793; LUCA.
eggNOG; COG3285; LUCA.
HOGENOM; HOG000008893; -.
InParanoid; O34398; -.
KO; K01971; -.
OMA; AMMVEDH; -.
PhylomeDB; O34398; -.
BioCyc; BSUB:BSU13400-MONOMER; -.
Proteomes; UP000001570; Chromosome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
CDD; cd04866; LigD_Pol_like_3; 1.
InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
InterPro; IPR014146; LigD_ligase_dom.
InterPro; IPR033652; LigD_Pol-like_3.
InterPro; IPR014145; LigD_pol_dom.
InterPro; IPR014143; NHEJ_ligase_prk.
Pfam; PF01068; DNA_ligase_A_M; 1.
TIGRFAMs; TIGR02778; ligD_pol; 1.
TIGRFAMs; TIGR02779; NHEJ_ligase_lig; 1.
TIGRFAMs; TIGR02776; NHEJ_ligase_prk; 1.
PROSITE; PS50160; DNA_LIGASE_A3; 1.
2: Evidence at transcript level;
ATP-binding; Complete proteome; DNA damage; DNA recombination;
DNA repair; DNA-binding; DNA-directed DNA polymerase; Exonuclease;
Hydrolase; Ligase; Manganese; Metal-binding; Multifunctional enzyme;
Nuclease; Nucleotide-binding; Nucleotidyltransferase;
Reference proteome; Sporulation; Transferase.
CHAIN 1 611 Bifunctional non-homologous end joining
protein LigD.
/FTId=PRO_0000389505.
REGION 5 310 Ligase domain (Lig).
REGION 325 564 DNA repair polymerase domain (Pol).
ACT_SITE 24 24 N6-AMP-lysine intermediate.
{ECO:0000250}.
METAL 26 26 Manganese 1. {ECO:0000250}.
METAL 184 184 Manganese 1. {ECO:0000250}.
METAL 439 439 Manganese 2. {ECO:0000250}.
METAL 439 439 Manganese 3. {ECO:0000250}.
METAL 441 441 Manganese 2. {ECO:0000250}.
METAL 441 441 Manganese 3. {ECO:0000250}.
METAL 530 530 Manganese 3. {ECO:0000250}.
BINDING 22 22 ATP. {ECO:0000250}.
BINDING 29 29 ATP. {ECO:0000250}.
BINDING 44 44 ATP. {ECO:0000250}.
BINDING 78 78 ATP. {ECO:0000250}.
BINDING 119 119 ATP. {ECO:0000250}.
BINDING 200 200 ATP. {ECO:0000250}.
BINDING 206 206 ATP. {ECO:0000250}.
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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