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SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS (dUTPase) (EC 3.6.1.23) (dUTP pyrophosphatase)

 YOSS_BACSU              Reviewed;         142 AA.
O34919; Q7BVP9;
24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
01-JAN-1998, sequence version 1.
25-OCT-2017, entry version 109.
RecName: Full=SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS;
Short=dUTPase;
EC=3.6.1.23;
AltName: Full=dUTP pyrophosphatase;
Name=yosS; Synonyms=yojU; OrderedLocusNames=BSU20020;
Bacillus subtilis (strain 168).
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
NCBI_TaxID=224308;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=168;
PubMed=9679200; DOI=10.1093/dnares/5.2.121;
Ghim S.-Y., Choi S.-K., Shin B.-S., Park S.-H.;
"An 8 kb nucleotide sequence at the 3' flanking region of the sspC
gene (184 degrees) on the Bacillus subtilis 168 chromosome containing
an intein and an intron.";
DNA Res. 5:121-126(1998).
[2]
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).
[3]
BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
PubMed=15939294; DOI=10.1016/j.pep.2005.02.013;
Persson R., McGeehan J., Wilson K.S.;
"Cloning, expression, purification, and characterisation of the
dUTPase encoded by the integrated Bacillus subtilis temperate
bacteriophage SPbeta.";
Protein Expr. Purif. 42:92-99(2005).
[4]
PRELIMINARY CRYSTALLIZATION.
PubMed=11375514; DOI=10.1107/S0907444901007727;
Persson R., Harkiolaki M., McGeehan J., Wilson K.S.;
"Crystallization and preliminary crystallographic analysis of
deoxyuridine 5'-triphosphate nucleotidohydrolase from Bacillus
subtilis.";
Acta Crystallogr. D 57:876-878(2001).
[5]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
PubMed=19342774; DOI=10.1107/S1744309109006228;
Li G.-L., Wang J., Li L.-F., Su X.-D.;
"Crystallization and preliminary X-ray analysis of three dUTPases from
Gram-positive bacteria.";
Acta Crystallogr. F 65:339-342(2009).
-!- FUNCTION: This enzyme is involved in nucleotide metabolism: it
produces dUMP, the immediate precursor of thymidine nucleotides
and it decreases the intracellular concentration of dUTP so that
uracil cannot be incorporated into DNA.
-!- CATALYTIC ACTIVITY: dUTP + H(2)O = dUMP + diphosphate.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:15939294};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.6 uM for dUTP {ECO:0000269|PubMed:15939294};
pH dependence:
Optimum pH is 5.5. {ECO:0000269|PubMed:15939294};
-!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP
(dUTP route): step 2/2.
-!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:15939294}.
-!- SIMILARITY: Belongs to the dUTPase family. {ECO:0000305}.
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EMBL; AF012906; AAB92488.1; -; Genomic_DNA.
EMBL; AL009126; CAB13893.1; -; Genomic_DNA.
RefSeq; NP_389883.1; NC_000964.3.
RefSeq; WP_004399492.1; NZ_JNCM01000036.1.
PDB; 2BAZ; X-ray; 2.30 A; A/B/C=1-142.
PDB; 2XX6; X-ray; 1.74 A; A/B/C/D=1-142.
PDB; 2XY3; X-ray; 2.55 A; A/B/C/D/E/F=1-142.
PDB; 2Y1T; X-ray; 1.89 A; A/B/C/D/E/F=1-142.
PDB; 4AO5; X-ray; 1.60 A; A/B/C/D/E/F=1-142.
PDBsum; 2BAZ; -.
PDBsum; 2XX6; -.
PDBsum; 2XY3; -.
PDBsum; 2Y1T; -.
PDBsum; 4AO5; -.
ProteinModelPortal; O34919; -.
SMR; O34919; -.
STRING; 224308.Bsubs1_010100011066; -.
PaxDb; O34919; -.
PRIDE; O34919; -.
EnsemblBacteria; CAB13893; CAB13893; BSU20020.
GeneID; 939536; -.
KEGG; bsu:BSU20020; -.
PATRIC; fig|224308.179.peg.2190; -.
eggNOG; ENOG4107YUK; Bacteria.
eggNOG; COG0756; LUCA.
HOGENOM; HOG000028966; -.
InParanoid; O34919; -.
KO; K01520; -.
PhylomeDB; O34919; -.
BioCyc; BSUB:BSU20020-MONOMER; -.
UniPathway; UPA00610; UER00666.
EvolutionaryTrace; O34919; -.
Proteomes; UP000001570; Chromosome.
GO; GO:0004170; F:dUTP diphosphatase activity; IDA:UniProtKB.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0006226; P:dUMP biosynthetic process; IDA:UniProtKB.
GO; GO:0046081; P:dUTP catabolic process; IDA:UniProtKB.
GO; GO:0070207; P:protein homotrimerization; IDA:UniProtKB.
CDD; cd07557; trimeric_dUTPase; 1.
InterPro; IPR029054; dUTPase-like.
InterPro; IPR036157; dUTPase-like_sf.
InterPro; IPR033704; dUTPase_trimeric.
Pfam; PF00692; dUTPase; 1.
SUPFAM; SSF51283; SSF51283; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Hydrolase; Magnesium; Metal-binding;
Nucleotide metabolism; Reference proteome.
CHAIN 1 142 SPBc2 prophage-derived deoxyuridine 5'-
triphosphate nucleotidohydrolase YosS.
/FTId=PRO_0000389002.
REGION 61 63 Substrate binding. {ECO:0000250}.
REGION 78 80 Substrate binding. {ECO:0000250}.
BINDING 74 74 Substrate. {ECO:0000250}.
STRAND 2 9 {ECO:0000244|PDB:4AO5}.
STRAND 18 20 {ECO:0000244|PDB:4AO5}.
STRAND 24 27 {ECO:0000244|PDB:4AO5}.
STRAND 32 34 {ECO:0000244|PDB:4AO5}.
STRAND 39 49 {ECO:0000244|PDB:4AO5}.
STRAND 54 60 {ECO:0000244|PDB:4AO5}.
HELIX 64 68 {ECO:0000244|PDB:4AO5}.
STRAND 70 72 {ECO:0000244|PDB:4AO5}.
STRAND 75 80 {ECO:0000244|PDB:4AO5}.
STRAND 89 98 {ECO:0000244|PDB:4AO5}.
STRAND 100 102 {ECO:0000244|PDB:4AO5}.
STRAND 107 115 {ECO:0000244|PDB:4AO5}.
STRAND 120 124 {ECO:0000244|PDB:4AO5}.
SEQUENCE 142 AA; 16148 MW; A986C4CCF2364B74 CRC64;
MQIKIKYLDE TQTRINKMEQ GDWIDLRAAE DVAIKKDEFK LVPLGVAMEL PEGYEAHVVP
RSSTYKNFGV IQTNSMGVID ESYKGDNDFW FFPAYALRDT KIKKGDRICQ FRIMKKMPAV
DLIEVDRLGN GDRGGHGSTG TK


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