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 03-AUG-2022, entry version 111.
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., 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; O34398; -.
DR PRIDE; O34398; -.
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 PhylomeDB; O34398; -.
DR BioCyc; BSUB:BSU13400-MON; -.
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; 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
