YTKD_BACSU
ID YTKD_BACSU Reviewed; 158 AA.
AC O35013; Q795N9;
DT 21-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Putative 8-oxo-dGTP diphosphatase YtkD;
DE Short=8-oxo-dGTPase;
DE EC=3.6.1.55;
DE AltName: Full=7,8-dihydro-8-oxoguanine-triphosphatase;
DE AltName: Full=dGTP pyrophosphohydrolase;
GN Name=ytkD; Synonyms=mutTA; OrderedLocusNames=BSU30630;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9387221; DOI=10.1099/00221287-143-11-3431;
RA Lapidus A., Galleron N., Sorokin A., Ehrlich S.D.;
RT "Sequencing and functional annotation of the Bacillus subtilis genes in the
RT 200 kb rrnB-dnaB region.";
RL Microbiology 143:3431-3441(1997).
RN [2]
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 [3]
RP FUNCTION, REGULATION, AND EXPRESSION.
RX PubMed=14761999; DOI=10.1128/jb.186.4.1050-1059.2004;
RA Ramirez M.I., Castellanos-Juarez F.X., Yasbin R.E., Pedraza-Reyes M.;
RT "The ytkD (mutTA) gene of Bacillus subtilis encodes a functional
RT antimutator 8-Oxo-(dGTP/GTP)ase and is under dual control of sigma A and
RT sigma F RNA polymerases.";
RL J. Bacteriol. 186:1050-1059(2004).
RN [4]
RP FUNCTION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=15576788; DOI=10.1128/jb.186.24.8380-8384.2004;
RA Xu W., Jones C.R., Dunn C.A., Bessman M.J.;
RT "Gene ytkD of Bacillus subtilis encodes an atypical nucleoside
RT triphosphatase member of the Nudix hydrolase superfamily.";
RL J. Bacteriol. 186:8380-8384(2004).
RN [5]
RP DISRUPTION PHENOTYPE IN GROWING CELLS.
RC STRAIN=168 / PS832;
RX PubMed=16513759; DOI=10.1128/jb.188.6.2285-2289.2006;
RA Castellanos-Juarez F.X., Alvarez-Alvarez C., Yasbin R.E., Setlow B.,
RA Setlow P., Pedraza-Reyes M.;
RT "YtkD and MutT protect vegetative cells but not spores of Bacillus subtilis
RT from oxidative stress.";
RL J. Bacteriol. 188:2285-2289(2006).
RN [6]
RP DISRUPTION PHENOTYPE IN STATIONARY PHASE CELLS.
RC STRAIN=168 / YB955;
RX PubMed=19011023; DOI=10.1128/jb.01210-08;
RA Vidales L.E., Cardenas L.C., Robleto E., Yasbin R.E., Pedraza-Reyes M.;
RT "Defects in the error prevention oxidized guanine system potentiate
RT stationary-phase mutagenesis in Bacillus subtilis.";
RL J. Bacteriol. 191:506-513(2009).
CC -!- FUNCTION: Involved in the GO system responsible for removing an
CC oxidatively damaged form of guanine (7,8-dihydro-8-oxoguanine, 8-oxo-
CC dGTP) from DNA and the nucleotide pool. 8-oxo-dGTP is inserted opposite
CC dA and dC residues of template DNA with almost equal efficiency thus
CC leading to A.T to G.C transversions (By similarity). Functions, in
CC conjunction with MutT, to protect vegetatively growing cells from DNA-
CC damaging agents such as H(2)O(2) or t-BHP (t-butylhydroperoxide). The 2
CC proteins do not however protect spores. According to PubMed:15576788,
CC phosphohydrolase that catalyzes the hydrolysis of all common nucleoside
CC triphosphates as well as of the mutagenic analog 8-oxo-dGTP. The high
CC catalytic efficiency on dGTP is in contrast to results from
CC PubMed:14761999. According to PubMed:14761999, catalyzes the hydrolysis
CC of 8-oxo-dGTP with a specific activity 413 times higher than that
CC exhibited against dGTP. Preferentially catalyzes the hydrolysis of 8-
CC oxo-dGTP and 8-oxo-GTP. According to PubMed:15576788, hydrolyzes
CC nucleoside triphosphates in a stepwise fashion through the diphosphate
CC to the monophosphate, releasing two molecules of inorganic
CC orthophosphate. {ECO:0000250, ECO:0000269|PubMed:14761999,
CC ECO:0000269|PubMed:15576788}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=8-oxo-dGTP + H2O = 8-oxo-dGMP + diphosphate + H(+);
CC Xref=Rhea:RHEA:31575, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:63224, ChEBI:CHEBI:77896; EC=3.6.1.55;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC -!- ACTIVITY REGULATION: Not induced by oxidative damage (following
CC treatment with paraquat or hydrogen peroxide). Not induced by mitomycin
CC C. Not induced by sigma-B general stress inducers such as sodium
CC chloride, ethanol or heat.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.16 mM for dGTP {ECO:0000269|PubMed:15576788};
CC KM=0.43 mM for 8-oxo-dGTP {ECO:0000269|PubMed:15576788};
CC KM=0.89 mM for dATP {ECO:0000269|PubMed:15576788};
CC Vmax=2.4 umol/min/mg enzyme with dGTP as substrate
CC {ECO:0000269|PubMed:15576788};
CC Vmax=3.1 umol/min/mg enzyme with 8-oxo-dGTP as substrate
CC {ECO:0000269|PubMed:15576788};
CC Vmax=4.7 umol/min/mg enzyme with dATP as substrate
CC {ECO:0000269|PubMed:15576788};
CC pH dependence:
CC Optimum pH is 8.5-9. {ECO:0000269|PubMed:15576788};
CC -!- DEVELOPMENTAL STAGE: Expressed during both vegetative growth and early
CC stage of sporulation.
CC -!- DISRUPTION PHENOTYPE: Growing cells lacking this gene have a 4-fold
CC increased spontaneous mutation frequency (a mild mutator phenotype), as
CC well as an increased sensitivity to DNA-damaging agents such as
CC H(2)O(2) or t-BHP. These phenotypes are increased in a double ytkD/mutT
CC disruption (PubMed:16513759). They are also seen in stationary phase
CC cells. Triple ytkD/mutM/mutY disrupted strains show increased mutation
CC rates during exponential and stationary phase (PubMed:19011023).
CC {ECO:0000269|PubMed:16513759, ECO:0000269|PubMed:19011023}.
CC -!- MISCELLANEOUS: According to PubMed:14761999, can complement an E.coli
CC mutT mutant. According to PubMed:15576788, cannot complement an E.coli
CC mutT mutant.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. {ECO:0000305}.
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DR EMBL; AF008220; AAC00239.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15041.1; -; Genomic_DNA.
DR PIR; E69994; E69994.
DR RefSeq; NP_390941.1; NC_000964.3.
DR RefSeq; WP_003229087.1; NZ_JNCM01000036.1.
DR PDB; 4JZS; X-ray; 2.20 A; A/D=1-158.
DR PDB; 4JZT; X-ray; 2.90 A; A/D=1-158.
DR PDB; 4JZU; X-ray; 1.70 A; A/B=1-158.
DR PDB; 4JZV; X-ray; 2.20 A; A/B=1-158.
DR PDBsum; 4JZS; -.
DR PDBsum; 4JZT; -.
DR PDBsum; 4JZU; -.
DR PDBsum; 4JZV; -.
DR AlphaFoldDB; O35013; -.
DR SMR; O35013; -.
DR STRING; 224308.BSU30630; -.
DR PaxDb; O35013; -.
DR PRIDE; O35013; -.
DR EnsemblBacteria; CAB15041; CAB15041; BSU_30630.
DR GeneID; 937072; -.
DR KEGG; bsu:BSU30630; -.
DR PATRIC; fig|224308.179.peg.3320; -.
DR eggNOG; COG0494; Bacteria.
DR InParanoid; O35013; -.
DR OMA; WVICRYG; -.
DR PhylomeDB; O35013; -.
DR BioCyc; BSUB:BSU30630-MON; -.
DR BioCyc; MetaCyc:BSU30630-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0035539; F:8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0016818; F:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR CDD; cd04665; Nudix_Hydrolase_8; 1.
DR InterPro; IPR020476; Nudix_hydrolase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR InterPro; IPR014078; Nudix_YtkD.
DR Pfam; PF00293; NUDIX; 1.
DR PRINTS; PR00502; NUDIXFAMILY.
DR SUPFAM; SSF55811; SSF55811; 1.
DR TIGRFAMs; TIGR02705; nudix_YtkD; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..158
FT /note="Putative 8-oxo-dGTP diphosphatase YtkD"
FT /id="PRO_0000057074"
FT DOMAIN 6..145
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 53..74
FT /note="Nudix box"
FT BINDING 68
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 72
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 11..21
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 26..34
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 37..43
FT /evidence="ECO:0007829|PDB:4JZU"
FT TURN 44..46
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 47..49
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:4JZV"
FT HELIX 61..73
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 75..89
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 94..107
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 114..124
FT /evidence="ECO:0007829|PDB:4JZU"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:4JZU"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:4JZU"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:4JZT"
FT HELIX 143..154
FT /evidence="ECO:0007829|PDB:4JZU"
SQ SEQUENCE 158 AA; 18512 MW; F4AC08535F32CBD0 CRC64;
MYEFKDYYQN TVQLSFDDQP FSDSPKHVWV ICRFGGKWLL TEHEDRGYEF PGGKVEPMEC
AEEAALREVK EETGARVKSL KYLGQYKVLG KEKVIVKNIY FADIEKLEKQ ADYFETKGPV
LFHELPENLS RNKKFSFIMK DSVLPISLKK LKESGWIE
