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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

Pathwayi

Sites

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

GO - Molecular functioni

  1. dUTP diphosphatase activity Source: UniProtKB
  2. magnesium ion binding Source: UniProtKB

GO - Biological processi

  1. dUMP biosynthetic process Source: UniProtKB
  2. dUTP catabolic process Source: UniProtKB
  3. 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.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: GO_Central
Complete GO annotation...

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.BSU20020.

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.

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.

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.BSU20020.

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: March 4, 2015
This is version 96 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.