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Protein

SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS

Gene

yosS

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

dUTP + H2O = dUMP + diphosphate.

Cofactori

Mg2+1 Publication

Kineticsi

  1. KM=0.6 µM for dUTP1 Publication

    pH dependencei

    Optimum pH is 5.5.1 Publication

    Pathway: dUMP biosynthesis

    This protein is involved in step 2 of the subpathway that synthesizes dUMP from dCTP (dUTP route).
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS (yosS), Probable deoxyuridine 5'-triphosphate nucleotidohydrolase YncF (yncF)
    This subpathway is part of the pathway dUMP biosynthesis, which is itself part of Pyrimidine metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes dUMP from dCTP (dUTP route), the pathway dUMP biosynthesis and in Pyrimidine metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei74 – 741SubstrateBy similarity

    GO - Molecular functioni

    • dUTP diphosphatase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB

    GO - Biological processi

    • dUMP biosynthetic process Source: UniProtKB
    • dUTP catabolic process Source: UniProtKB
    • protein homotrimerization Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Nucleotide metabolism

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciBSUB:BSU20020-MONOMER.
    UniPathwayiUPA00610; UER00666.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS (EC:3.6.1.23)
    Short name:
    dUTPase
    Alternative name(s):
    dUTP pyrophosphatase
    Gene namesi
    Name:yosS
    Synonyms:yojU
    Ordered Locus Names:BSU20020
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570 Componenti: Chromosome

    Organism-specific databases

    GenoListiBSU20020.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 142142SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosSPRO_0000389002Add
    BLAST

    Proteomic databases

    PaxDbiO34919.

    Interactioni

    Subunit structurei

    Homotrimer.1 Publication

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100011066.

    Structurei

    Secondary structure

    1
    142
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 98Combined sources
    Beta strandi18 – 203Combined sources
    Beta strandi24 – 274Combined sources
    Beta strandi32 – 343Combined sources
    Beta strandi39 – 4911Combined sources
    Beta strandi54 – 607Combined sources
    Helixi64 – 685Combined sources
    Beta strandi70 – 723Combined sources
    Beta strandi75 – 806Combined sources
    Beta strandi89 – 9810Combined sources
    Beta strandi100 – 1023Combined sources
    Beta strandi107 – 1159Combined sources
    Beta strandi120 – 1245Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2BAZX-ray2.30A/B/C1-142[»]
    2XX6X-ray1.74A/B/C/D1-142[»]
    2XY3X-ray2.55A/B/C/D/E/F1-142[»]
    2Y1TX-ray1.89A/B/C/D/E/F1-142[»]
    4AO5X-ray1.60A/B/C/D/E/F1-142[»]
    ProteinModelPortaliO34919.
    SMRiO34919. Positions 1-128.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO34919.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni61 – 633Substrate bindingBy similarity
    Regioni78 – 803Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the dUTPase family.Curated

    Phylogenomic databases

    eggNOGiCOG0756.
    HOGENOMiHOG000028966.
    InParanoidiO34919.
    KOiK01520.
    OrthoDBiEOG689HXK.
    PhylomeDBiO34919.

    Family and domain databases

    Gene3Di2.70.40.10. 1 hit.
    InterProiIPR029054. dUTPase-like.
    IPR008180. dUTPase/dCTP_deaminase.
    [Graphical view]
    PfamiPF00692. dUTPase. 1 hit.
    [Graphical view]
    SUPFAMiSSF51283. SSF51283. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O34919-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQIKIKYLDE TQTRINKMEQ GDWIDLRAAE DVAIKKDEFK LVPLGVAMEL
    60 70 80 90 100
    PEGYEAHVVP RSSTYKNFGV IQTNSMGVID ESYKGDNDFW FFPAYALRDT
    110 120 130 140
    KIKKGDRICQ FRIMKKMPAV DLIEVDRLGN GDRGGHGSTG TK
    Length:142
    Mass (Da):16,148
    Last modified:January 1, 1998 - v1
    Checksum:iA986C4CCF2364B74
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF012906 Genomic DNA. Translation: AAB92488.1.
    AL009126 Genomic DNA. Translation: CAB13893.1.
    RefSeqiNP_389883.1. NC_000964.3.
    WP_004399492.1. NZ_JNCM01000036.1.

    Genome annotation databases

    EnsemblBacteriaiCAB13893; CAB13893; BSU20020.
    GeneIDi939536.
    KEGGibsu:BSU20020.
    PATRICi18975849. VBIBacSub10457_2115.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF012906 Genomic DNA. Translation: AAB92488.1.
    AL009126 Genomic DNA. Translation: CAB13893.1.
    RefSeqiNP_389883.1. NC_000964.3.
    WP_004399492.1. NZ_JNCM01000036.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2BAZX-ray2.30A/B/C1-142[»]
    2XX6X-ray1.74A/B/C/D1-142[»]
    2XY3X-ray2.55A/B/C/D/E/F1-142[»]
    2Y1TX-ray1.89A/B/C/D/E/F1-142[»]
    4AO5X-ray1.60A/B/C/D/E/F1-142[»]
    ProteinModelPortaliO34919.
    SMRiO34919. Positions 1-128.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100011066.

    Proteomic databases

    PaxDbiO34919.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB13893; CAB13893; BSU20020.
    GeneIDi939536.
    KEGGibsu:BSU20020.
    PATRICi18975849. VBIBacSub10457_2115.

    Organism-specific databases

    GenoListiBSU20020.

    Phylogenomic databases

    eggNOGiCOG0756.
    HOGENOMiHOG000028966.
    InParanoidiO34919.
    KOiK01520.
    OrthoDBiEOG689HXK.
    PhylomeDBiO34919.

    Enzyme and pathway databases

    UniPathwayiUPA00610; UER00666.
    BioCyciBSUB:BSU20020-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiO34919.

    Family and domain databases

    Gene3Di2.70.40.10. 1 hit.
    InterProiIPR029054. dUTPase-like.
    IPR008180. dUTPase/dCTP_deaminase.
    [Graphical view]
    PfamiPF00692. dUTPase. 1 hit.
    [Graphical view]
    SUPFAMiSSF51283. SSF51283. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "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."
      Ghim S.-Y., Choi S.-K., Shin B.-S., Park S.-H.
      DNA Res. 5:121-126(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      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.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "Cloning, expression, purification, and characterisation of the dUTPase encoded by the integrated Bacillus subtilis temperate bacteriophage SPbeta."
      Persson R., McGeehan J., Wilson K.S.
      Protein Expr. Purif. 42:92-99(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT.
    4. "Crystallization and preliminary crystallographic analysis of deoxyuridine 5'-triphosphate nucleotidohydrolase from Bacillus subtilis."
      Persson R., Harkiolaki M., McGeehan J., Wilson K.S.
      Acta Crystallogr. D 57:876-878(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: PRELIMINARY CRYSTALLIZATION.
    5. "Crystallization and preliminary X-ray analysis of three dUTPases from Gram-positive bacteria."
      Li G.-L., Wang J., Li L.-F., Su X.-D.
      Acta Crystallogr. F 65:339-342(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).

    Entry informationi

    Entry nameiYOSS_BACSU
    AccessioniPrimary (citable) accession number: O34919
    Secondary accession number(s): Q7BVP9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 24, 2009
    Last sequence update: January 1, 1998
    Last modified: June 24, 2015
    This is version 98 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.