YOSS_BACSU
ID YOSS_BACSU Reviewed; 142 AA.
AC O34919; Q7BVP9;
DT 24-NOV-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=SPbeta prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS;
DE Short=dUTPase {ECO:0000303|PubMed:9679200};
DE EC=3.6.1.23 {ECO:0000269|PubMed:15939294};
DE AltName: Full=dUTP pyrophosphatase;
GN Name=yosS {ECO:0000303|PubMed:9679200}; Synonyms=yojU;
GN OrderedLocusNames=BSU20020;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9679200; DOI=10.1093/dnares/5.2.121;
RA Ghim S.-Y., Choi S.-K., Shin B.-S., Park S.-H.;
RT "An 8 kb nucleotide sequence at the 3' flanking region of the sspC gene
RT (184 degrees) on the Bacillus subtilis 168 chromosome containing an intein
RT and an intron.";
RL DNA Res. 5:121-126(1998).
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 CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=15939294; DOI=10.1016/j.pep.2005.02.013;
RA Persson R., McGeehan J., Wilson K.S.;
RT "Cloning, expression, purification, and characterisation of the dUTPase
RT encoded by the integrated Bacillus subtilis temperate bacteriophage
RT SPbeta.";
RL Protein Expr. Purif. 42:92-99(2005).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=17114254; DOI=10.1128/jb.01381-06;
RA Thomaides H.B., Davison E.J., Burston L., Johnson H., Brown D.R.,
RA Hunt A.C., Errington J., Czaplewski L.;
RT "Essential bacterial functions encoded by gene pairs.";
RL J. Bacteriol. 189:591-602(2007).
RN [5]
RP PRELIMINARY CRYSTALLIZATION.
RX PubMed=11375514; DOI=10.1107/s0907444901007727;
RA Persson R., Harkiolaki M., McGeehan J., Wilson K.S.;
RT "Crystallization and preliminary crystallographic analysis of deoxyuridine
RT 5'-triphosphate nucleotidohydrolase from Bacillus subtilis.";
RL Acta Crystallogr. D 57:876-878(2001).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
RX PubMed=19342774; DOI=10.1107/s1744309109006228;
RA Li G.-L., Wang J., Li L.-F., Su X.-D.;
RT "Crystallization and preliminary X-ray analysis of three dUTPases from
RT Gram-positive bacteria.";
RL Acta Crystallogr. F 65:339-342(2009).
RN [7] {ECO:0007744|PDB:2XX6, ECO:0007744|PDB:2XY3, ECO:0007744|PDB:2Y1T}
RP X-RAY CRYSTALLOGRAPHY (1.74 ANGSTROMS) ALONE AND IN COMPLEX WITH SUBSTRATE
RP ANALOGS, PROBABLE ACTIVE SITE, COFACTOR, SUBUNIT, AND DOMAIN.
RC STRAIN=168;
RX PubMed=21358047; DOI=10.1107/s0907444911003234;
RA Garcia-Nafria J., Harkiolaki M., Persson R., Fogg M.J., Wilson K.S.;
RT "The structure of Bacillus subtilis SPbeta prophage dUTPase and its
RT complexes with two nucleotides.";
RL Acta Crystallogr. D 67:167-175(2011).
RN [8] {ECO:0007744|PDB:4AO5}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH DUMP, PROBABLE
RP ACTIVE SITE, COFACTOR, AND SUBUNIT.
RX PubMed=23897460; DOI=10.1107/s090744491300735x;
RA Garcia-Nafria J., Timm J., Harrison C., Turkenburg J.P., Wilson K.S.;
RT "Tying down the arm in Bacillus dUTPase: structure and mechanism.";
RL Acta Crystallogr. D 69:1367-1380(2013).
CC -!- FUNCTION: Involved in nucleotide metabolism: produces dUMP, the
CC immediate precursor of thymidine nucleotides and decreases the
CC intracellular concentration of dUTP, so that uracil cannot be
CC incorporated into DNA (PubMed:9679200). The Ser-62 side chain changes
CC its position upon ligand-binding to make contacts with the nucleotide
CC phosphates (PubMed:21358047). {ECO:0000269|PubMed:21358047,
CC ECO:0000269|PubMed:9679200}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dUTP + H2O = diphosphate + dUMP + H(+); Xref=Rhea:RHEA:10248,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:61555, ChEBI:CHEBI:246422; EC=3.6.1.23;
CC Evidence={ECO:0000269|PubMed:15939294};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15939294, ECO:0000269|PubMed:21358047};
CC Note=Binds 1 Mg(2+) per subunit, coordinated entirely by the nucleotide
CC and ordered water molecules. {ECO:0000269|PubMed:21358047};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.6 uM for dUTP {ECO:0000269|PubMed:15939294};
CC pH dependence:
CC Optimum pH is 5.5. {ECO:0000269|PubMed:15939294};
CC -!- PATHWAY: Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP
CC route): step 2/2.
CC -!- SUBUNIT: Homotrimer. {ECO:0000269|PubMed:15939294,
CC ECO:0000269|PubMed:21358047, ECO:0000269|PubMed:23897460}.
CC -!- DOMAIN: The uracil deoxyribose moiety interacts with the protein
CC through Ile-79 and Tyr-83, which discriminate against the ribose form
CC of the nucleotide. {ECO:0000269|PubMed:21358047}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype; double yncF-yosS deletions
CC (both encode dUTPases) are also viable. {ECO:0000269|PubMed:17114254}.
CC -!- SIMILARITY: Belongs to the dUTPase family. {ECO:0000305}.
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DR EMBL; AF012906; AAB92488.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13893.1; -; Genomic_DNA.
DR RefSeq; NP_389883.1; NC_000964.3.
DR RefSeq; WP_004399492.1; NZ_JNCM01000036.1.
DR PDB; 2BAZ; X-ray; 2.30 A; A/B/C=1-142.
DR PDB; 2XX6; X-ray; 1.74 A; A/B/C/D=1-142.
DR PDB; 2XY3; X-ray; 2.55 A; A/B/C/D/E/F=1-142.
DR PDB; 2Y1T; X-ray; 1.89 A; A/B/C/D/E/F=1-142.
DR PDB; 4AO5; X-ray; 1.60 A; A/B/C/D/E/F=1-142.
DR PDBsum; 2BAZ; -.
DR PDBsum; 2XX6; -.
DR PDBsum; 2XY3; -.
DR PDBsum; 2Y1T; -.
DR PDBsum; 4AO5; -.
DR AlphaFoldDB; O34919; -.
DR SMR; O34919; -.
DR STRING; 224308.BSU20020; -.
DR PaxDb; O34919; -.
DR PRIDE; O34919; -.
DR EnsemblBacteria; CAB13893; CAB13893; BSU_20020.
DR GeneID; 939536; -.
DR KEGG; bsu:BSU20020; -.
DR PATRIC; fig|224308.179.peg.2190; -.
DR eggNOG; COG0756; Bacteria.
DR InParanoid; O34919; -.
DR PhylomeDB; O34919; -.
DR BioCyc; BSUB:BSU20020-MON; -.
DR BRENDA; 3.6.1.23; 658.
DR UniPathway; UPA00610; UER00666.
DR EvolutionaryTrace; O34919; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0032991; C:protein-containing complex; IDA:UniProtKB.
DR GO; GO:0004170; F:dUTP diphosphatase activity; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0006226; P:dUMP biosynthetic process; IDA:UniProtKB.
DR GO; GO:0046081; P:dUTP catabolic process; IDA:UniProtKB.
DR CDD; cd07557; trimeric_dUTPase; 1.
DR Gene3D; 2.70.40.10; -; 1.
DR InterPro; IPR008181; dUTPase.
DR InterPro; IPR029054; dUTPase-like.
DR InterPro; IPR036157; dUTPase-like_sf.
DR InterPro; IPR033704; dUTPase_trimeric.
DR PANTHER; PTHR11241; PTHR11241; 1.
DR Pfam; PF00692; dUTPase; 1.
DR SUPFAM; SSF51283; SSF51283; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Nucleotide metabolism;
KW Reference proteome.
FT CHAIN 1..142
FT /note="SPbeta prophage-derived deoxyuridine 5'-triphosphate
FT nucleotidohydrolase YosS"
FT /id="PRO_0000389002"
FT ACT_SITE 80
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:21358047,
FT ECO:0000305|PubMed:23897460"
FT BINDING 62
FT /ligand="dUMP"
FT /ligand_id="ChEBI:CHEBI:246422"
FT /evidence="ECO:0000269|PubMed:23897460,
FT ECO:0007744|PDB:4AO5"
FT BINDING 74
FT /ligand="dUMP"
FT /ligand_id="ChEBI:CHEBI:246422"
FT /evidence="ECO:0000269|PubMed:23897460,
FT ECO:0007744|PDB:4AO5"
FT BINDING 83
FT /ligand="dUMP"
FT /ligand_id="ChEBI:CHEBI:246422"
FT /evidence="ECO:0000269|PubMed:23897460,
FT ECO:0007744|PDB:4AO5"
FT BINDING 91
FT /ligand="dUMP"
FT /ligand_id="ChEBI:CHEBI:246422"
FT /evidence="ECO:0000269|PubMed:23897460,
FT ECO:0007744|PDB:4AO5"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 18..20
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 24..27
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 39..49
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 54..60
FT /evidence="ECO:0007829|PDB:4AO5"
FT HELIX 64..68
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 75..80
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 89..98
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 107..115
FT /evidence="ECO:0007829|PDB:4AO5"
FT STRAND 120..124
FT /evidence="ECO:0007829|PDB:4AO5"
SQ SEQUENCE 142 AA; 16148 MW; A986C4CCF2364B74 CRC64;
MQIKIKYLDE TQTRINKMEQ GDWIDLRAAE DVAIKKDEFK LVPLGVAMEL PEGYEAHVVP
RSSTYKNFGV IQTNSMGVID ESYKGDNDFW FFPAYALRDT KIKKGDRICQ FRIMKKMPAV
DLIEVDRLGN GDRGGHGSTG TK
