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P06968 (DUT_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 137. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Deoxyuridine 5'-triphosphate nucleotidohydrolase

Short name=dUTPase
EC=3.6.1.23
Alternative name(s):
dUTP pyrophosphatase
Gene names
Name:dut
Synonyms:dnaS, sof
Ordered Locus Names:b3640, JW3615
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length151 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. HAMAP-Rule MF_00116

Catalytic activity

dUTP + H2O = dUMP + diphosphate. HAMAP-Rule MF_00116

Cofactor

Magnesium. Ref.10

Pathway

Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 2/2. HAMAP-Rule MF_00116

Subunit structure

Homotrimer. Ref.10

Sequence similarities

Belongs to the dUTPase family.

Ontologies

Keywords
   Biological processNucleotide metabolism
   LigandMagnesium
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processdUMP biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

dUTP metabolic process

Inferred from electronic annotation. Source: InterPro

   Cellular_componentcytosol

Inferred from direct assay PubMed 16858726. Source: UniProtKB

   Molecular_functiondUTP diphosphatase activity

Inferred from direct assay PubMed 346589. Source: EcoCyc

magnesium ion binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 151151Deoxyuridine 5'-triphosphate nucleotidohydrolase HAMAP-Rule MF_00116
PRO_0000182858

Regions

Region70 – 723Substrate binding By similarity
Region87 – 893Substrate binding Probable

Sites

Binding site831Substrate
Binding site971Substrate; via amide nitrogen and carbonyl oxygen

Experimental info

Mutagenesis891D → N: Reduces catalytic activity 40000-fold. Ref.10

Secondary structure

........................... 151
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P06968 [UniParc].

Last modified April 1, 1988. Version 1.
Checksum: 98FA3DE0BC70FFB2

FASTA15116,155
        10         20         30         40         50         60 
MKKIDVKILD PRVGKEFPLP TYATSGSAGL DLRACLNDAV ELAPGDTTLV PTGLAIHIAD 

        70         80         90        100        110        120 
PSLAAMMLPR SGLGHKHGIV LGNLVGLIDS DYQGQLMISV WNRGQDSFTI QPGERIAQMI 

       130        140        150 
FVPVVQAEFN LVEDFDATDR GEGGFGHSGR Q 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequence of the structural gene for dUTPase of Escherichia coli K-12."
Lundberg L.G., Thoresson H.-O., Karlstroem O.H., Nyman P.O.
EMBO J. 2:967-971(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[6]"Crystal structure of a dUTPase."
Cedergren-Zeppezauer E.S., Larsson G., Nyman P.O., Dauter Z., Wilson K.S.
Nature 355:740-743(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[7]"Crystal structure of the Escherichia coli dUTPase in complex with a substrate analogue (dUDP)."
Larsson G., Svensson L.A., Nyman P.O.
Nat. Struct. Biol. 3:532-538(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[8]"The refined structure of dUTPase from Escherichia coli."
Dauter Z., Wilson K.S., Larsson G., Nyman P.O., Cedergren-Zeppezauer E.S.
Acta Crystallogr. D 54:735-749(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[9]"Atomic resolution structure of Escherichia coli dUTPase determined ab initio."
Gonzalez A., Larsson G., Persson R., Cedergren-Zeppezauer E.S.
Acta Crystallogr. D 57:767-774(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS).
[10]"Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase."
Barabas O., Pongracz V., Kovari J., Wilmanns M., Vertessy B.G.
J. Biol. Chem. 279:42907-42915(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH MAGNESIUM IONS AND SUBSTRATE, COFACTOR, MUTAGENESIS OF ASP-89, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X01714 Genomic DNA. Translation: CAA25859.1.
V01578 Genomic DNA. Translation: CAA24897.1.
L10328 Genomic DNA. Translation: AAA61993.1.
U00096 Genomic DNA. Translation: AAC76664.1.
AP009048 Genomic DNA. Translation: BAE77652.1.
PIRWPECDU. A30388.
RefSeqNP_418097.1. NC_000913.3.
YP_491793.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DUDX-ray2.30A1-151[»]
1DUPX-ray1.90A1-151[»]
1EU5X-ray1.45A1-151[»]
1EUWX-ray1.05A1-151[»]
1RN8X-ray1.93A1-151[»]
1RNJX-ray1.70A1-151[»]
1SEHX-ray1.47A1-151[»]
1SYLX-ray1.95A1-151[»]
2HR6X-ray1.84A1-151[»]
2HRMX-ray1.70A1-151[»]
DisProtDP00337.
ProteinModelPortalP06968.
SMRP06968. Positions 1-135.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP06968. 10 interactions.
MINTMINT-1279301.
STRING511145.b3640.

2D gel databases

SWISS-2DPAGEP06968.

Proteomic databases

PaxDbP06968.
PRIDEP06968.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76664; AAC76664; b3640.
BAE77652; BAE77652; BAE77652.
GeneID12934430.
948607.
KEGGecj:Y75_p3534.
eco:b3640.
PATRIC32122767. VBIEscCol129921_3760.

Organism-specific databases

EchoBASEEB0247.
EcoGeneEG10251. dut.

Phylogenomic databases

eggNOGCOG0756.
HOGENOMHOG000028968.
KOK01520.
OMAMVSAWNR.
OrthoDBEOG689HXK.
PhylomeDBP06968.
ProtClustDBPRK00601.

Enzyme and pathway databases

BioCycEcoCyc:DUTP-PYROP-MONOMER.
ECOL316407:JW3615-MONOMER.
MetaCyc:DUTP-PYROP-MONOMER.
UniPathwayUPA00610; UER00666.

Gene expression databases

GenevestigatorP06968.

Family and domain databases

HAMAPMF_00116. dUTPase_bact.
InterProIPR008180. dUTP_pyroPase.
IPR008181. dUTP_pyroPase_sf.
[Graphical view]
PfamPF00692. dUTPase. 1 hit.
[Graphical view]
TIGRFAMsTIGR00576. dut. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP06968.
PROP06968.

Entry information

Entry nameDUT_ECOLI
AccessionPrimary (citable) accession number: P06968
Secondary accession number(s): Q2M7V4
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: April 16, 2014
This is version 137 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene