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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-APR-2021, entry version 109.
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:
Reaction=ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-
(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP +
diphosphate.; EC=6.5.1.1;
-!- 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.
SMR; O34398; -.
STRING; 224308.BSU13400; -.
PaxDb; O34398; -.
PRIDE; O34398; -.
EnsemblBacteria; CAB13197; CAB13197; BSU_13400.
GeneID; 939372; -.
KEGG; bsu:BSU13400; -.
PATRIC; fig|224308.179.peg.1455; -.
eggNOG; COG1793; Bacteria.
eggNOG; COG3285; Bacteria.
InParanoid; O34398; -.
OMA; YMANLGC; -.
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; 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
/note="Bifunctional non-homologous end joining protein
LigD"
/id="PRO_0000389505"
REGION 5..310
/note="Ligase domain (Lig)"
REGION 325..564
/note="DNA repair polymerase domain (Pol)"
ACT_SITE 24
/note="N6-AMP-lysine intermediate"
/evidence="ECO:0000250"
METAL 26
/note="Manganese 1"
/evidence="ECO:0000250"
METAL 184
/note="Manganese 1"
/evidence="ECO:0000250"
METAL 439
/note="Manganese 2"
/evidence="ECO:0000250"
METAL 439
/note="Manganese 3"
/evidence="ECO:0000250"
METAL 441
/note="Manganese 2"
/evidence="ECO:0000250"
METAL 441
/note="Manganese 3"
/evidence="ECO:0000250"
METAL 530
/note="Manganese 3"
/evidence="ECO:0000250"
BINDING 22
/note="ATP"
/evidence="ECO:0000250"
BINDING 29
/note="ATP"
/evidence="ECO:0000250"
BINDING 44
/note="ATP"
/evidence="ECO:0000250"
BINDING 78
/note="ATP"
/evidence="ECO:0000250"
BINDING 119
/note="ATP"
/evidence="ECO:0000250"
BINDING 200
/note="ATP"
/evidence="ECO:0000250"
BINDING 206
/note="ATP"
/evidence="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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[Nhej1 Xlf] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[Polq Chaos1] DNA polymerase theta (EC 2.7.7.7) (Chromosome aberrations occurring spontaneously protein 1) (DNA polymerase eta)
[NHEJ1 XLF] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[mus-53 lig4 NCU06264] DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Mutagen-sensitive protein 53) (Polydeoxyribonucleotide synthase [ATP] 4)
[ORF1ab orf1ab] 2'-O-methyltransferase (EC 2.7.7.48) (EC 3.4.19.12) (EC 3.4.22.69) (EC 3.6.4.12) (EC 3.6.4.13) (3C-like proteinase) (Growth factor-like peptide) (Guanine-N7 methyltransferase) (Helicase) (Host translation inhibitor nsp1) (Leader protein) (NendoU) (Non-structural protein 10) (Non-structural protein 2) (Non-structural protein 3) (Non-structural protein 4) (Non-structural protein 6) (Non-structural protein 7) (Non-structural protein 8) (Non-structural protein 9) (ORF1ab polyprotein) (Papain-like proteinase) (RNA-directed RNA polymerase) (Replicase polyprotein 1ab) (Uridylate-specific endoribonuclease) (p65 homolog)
[PARP1 ADPRT PPOL] Poly [ADP-ribose] polymerase 1 (PARP-1) (EC 2.4.2.30) (ADP-ribosyltransferase diphtheria toxin-like 1) (ARTD1) (DNA ADP-ribosyltransferase PARP1) (EC 2.4.2.-) (NAD(+) ADP-ribosyltransferase 1) (ADPRT 1) (Poly[ADP-ribose] synthase 1) (Protein poly-ADP-ribosyltransferase PARP1) (EC 2.4.2.-)
[Parp1 Adprp Adprt Adprt1] Poly [ADP-ribose] polymerase 1 (PARP-1) (EC 2.4.2.30) (ADP-ribosyltransferase diphtheria toxin-like 1) (ARTD1) (DNA ADP-ribosyltransferase PARP1) (EC 2.4.2.-) (NAD(+) ADP-ribosyltransferase 1) (ADPRT 1) (Poly[ADP-ribose] synthase 1) (msPARP) (Protein poly-ADP-ribosyltransferase PARP1) (EC 2.4.2.-)
[PARP3 ADPRT3 ADPRTL3] Protein mono-ADP-ribosyltransferase PARP3 (EC 2.4.2.-) (ADP-ribosyltransferase diphtheria toxin-like 3) (ARTD3) (DNA ADP-ribosyltransferase PARP3) (EC 2.4.2.-) (IRT1) (NAD(+) ADP-ribosyltransferase 3) (ADPRT-3) (Poly [ADP-ribose] polymerase 3) (PARP-3) (hPARP-3) (Poly[ADP-ribose] synthase 3) (pADPRT-3)
[Parp3 Adprt3] Protein mono-ADP-ribosyltransferase PARP3 (EC 2.4.2.-) (ADP-ribosyltransferase diphtheria toxin-like 3) (ARTD3) (DNA ADP-ribosyltransferase PARP3) (EC 2.4.2.-) (NAD(+) ADP-ribosyltransferase 3) (ADPRT-3) (Poly [ADP-ribose] polymerase 3) (PARP-3) (Poly[ADP-ribose] synthase 3) (pADPRT-3)
[LIG6 At1g66730 F4N21.14] DNA ligase 6 (AtLIG6) (DNA ligase VI) (EC 6.5.1.1) (Ligase 1)
[Pnkp] Bifunctional polynucleotide phosphatase/kinase (DNA 5'-kinase/3'-phosphatase) (Polynucleotide kinase-3'-phosphatase) [Includes: Polynucleotide 3'-phosphatase (EC 3.1.3.32) (2'(3')-polynucleotidase); Polynucleotide 5'-hydroxyl-kinase (EC 2.7.1.78)]
[PRI2 YKL045W YKL258] DNA primase large subunit (DNA polymerase alpha:primase complex p58 subunit) (DNA polymerase-primase complex p58 subunit) (Pol alpha-primase complex p58 subunit) (DNA primase 58 kDa subunit)
[LIG1 At1g08130 T23G18.1 T6D22.23] DNA ligase 1 (AtLIG1) (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1)
[POL2 DUN2 YNL262W N0825] DNA polymerase epsilon catalytic subunit A (EC 2.7.7.7) (3'-5' exodeoxyribonuclease) (EC 3.1.11.-) (DNA polymerase II subunit A)
[Polr2a Rpii215 Rpo2-1] DNA-directed RNA polymerase II subunit RPB1 (RNA polymerase II subunit B1) (EC 2.7.7.6) (DNA-directed RNA polymerase II subunit A) (DNA-directed RNA polymerase III largest subunit)
[POLQ POLH] DNA polymerase theta (EC 2.7.7.7) (DNA polymerase eta)
[Pold1] DNA polymerase delta catalytic subunit (EC 2.7.7.7) (3'-5' exodeoxyribonuclease) (EC 3.1.11.-)
[Parp1 Adprt] Poly [ADP-ribose] polymerase 1 (PARP-1) (EC 2.4.2.30) (ADP-ribosyltransferase diphtheria toxin-like 1) (ARTD1) (DNA ADP-ribosyltransferase PARP1) (EC 2.4.2.-) (NAD(+) ADP-ribosyltransferase 1) (ADPRT 1) (Poly[ADP-ribose] synthase 1) (Protein poly-ADP-ribosyltransferase PARP1) (EC 2.4.2.-)
[PNKP] Bifunctional polynucleotide phosphatase/kinase (DNA 5'-kinase/3'-phosphatase) (Polynucleotide kinase-3'-phosphatase) [Includes: Polynucleotide 3'-phosphatase (EC 3.1.3.32) (2'(3')-polynucleotidase); Polynucleotide 5'-hydroxyl-kinase (EC 2.7.1.78)]
[Pole Pole1] DNA polymerase epsilon catalytic subunit A (EC 2.7.7.7) (3'-5' exodeoxyribonuclease) (EC 3.1.11.-) (DNA polymerase II subunit A)
[POLD1 POLD] DNA polymerase delta catalytic subunit (EC 2.7.7.7) (3'-5' exodeoxyribonuclease) (EC 3.1.11.-) (DNA polymerase subunit delta p125)
[lig APE_1094.1] DNA ligase (EC 6.5.1.7) (Polydeoxyribonucleotide synthase [ATP/ADP])
[POL3 CDC2 TEX1 YDL102W D2366] DNA polymerase delta catalytic subunit (EC 2.7.7.7) (3'-5' exodeoxyribonuclease) (EC 3.1.11.-) (DNA polymerase III)
[POLR2A POLR2] DNA-directed RNA polymerase II subunit RPB1 (RNA polymerase II subunit B1) (EC 2.7.7.6) (DNA-directed RNA polymerase II subunit A) (DNA-directed RNA polymerase III largest subunit) (RNA-directed RNA polymerase II subunit RPB1) (EC 2.7.7.48)

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