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Protein

Deoxyuridine 5'-triphosphate nucleotidohydrolase

Gene

dut

Organism
Escherichia coli (strain K12)
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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei83 – 831Substrate1 Publication
Binding sitei97 – 971Substrate; via amide nitrogen and carbonyl oxygen1 Publication

GO - Molecular functioni

  1. dUTP diphosphatase activity Source: EcoCyc
  2. magnesium ion binding Source: GO_Central

GO - Biological processi

  1. dUMP biosynthetic process Source: GO_Central
  2. dUTP catabolic process Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:DUTP-PYROP-MONOMER.
ECOL316407:JW3615-MONOMER.
MetaCyc:DUTP-PYROP-MONOMER.
BRENDAi3.6.1.23. 2026.
UniPathwayiUPA00610; UER00666.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC:3.6.1.23)
Short name:
dUTPase
Alternative name(s):
dUTP pyrophosphatase
Gene namesi
Name:dut
Synonyms:dnaS, sof
Ordered Locus Names:b3640, JW3615
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10251. dut.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi89 – 891D → N: Reduces catalytic activity 40000-fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 151151Deoxyuridine 5'-triphosphate nucleotidohydrolasePRO_0000182858Add
BLAST

Proteomic databases

PaxDbiP06968.
PRIDEiP06968.

2D gel databases

SWISS-2DPAGEP06968.

Expressioni

Gene expression databases

GenevestigatoriP06968.

Interactioni

Subunit structurei

Homotrimer.1 Publication

Protein-protein interaction databases

IntActiP06968. 11 interactions.
MINTiMINT-1279301.
STRINGi511145.b3640.

Structurei

Secondary structure

1
151
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 84Combined sources
Turni11 – 155Combined sources
Beta strandi30 – 334Combined sources
Beta strandi40 – 423Combined sources
Beta strandi47 – 5711Combined sources
Beta strandi63 – 697Combined sources
Helixi71 – 777Combined sources
Beta strandi79 – 813Combined sources
Beta strandi84 – 885Combined sources
Beta strandi94 – 1029Combined sources
Beta strandi104 – 1063Combined sources
Beta strandi108 – 1103Combined sources
Beta strandi115 – 1239Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
DisProtiDP00337.
ProteinModelPortaliP06968.
SMRiP06968. Positions 1-135.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06968.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni70 – 723Substrate bindingBy similarity
Regioni87 – 893Substrate bindingCurated

Sequence similaritiesi

Belongs to the dUTPase family.Curated

Phylogenomic databases

eggNOGiCOG0756.
HOGENOMiHOG000028968.
InParanoidiP06968.
KOiK01520.
OMAiILPRSGM.
OrthoDBiEOG689HXK.
PhylomeDBiP06968.

Family and domain databases

Gene3Di2.70.40.10. 1 hit.
HAMAPiMF_00116. dUTPase_bact.
InterProiIPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR008181. dUTPase_1.
[Graphical view]
PfamiPF00692. dUTPase. 1 hit.
[Graphical view]
SUPFAMiSSF51283. SSF51283. 1 hit.
TIGRFAMsiTIGR00576. dut. 1 hit.

Sequencei

Sequence statusi: Complete.

P06968-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKIDVKILD PRVGKEFPLP TYATSGSAGL DLRACLNDAV ELAPGDTTLV
60 70 80 90 100
PTGLAIHIAD PSLAAMMLPR SGLGHKHGIV LGNLVGLIDS DYQGQLMISV
110 120 130 140 150
WNRGQDSFTI QPGERIAQMI FVPVVQAEFN LVEDFDATDR GEGGFGHSGR

Q
Length:151
Mass (Da):16,155
Last modified:April 1, 1988 - v1
Checksum:i98FA3DE0BC70FFB2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA30388. WPECDU.
RefSeqiNP_418097.1. NC_000913.3.
YP_491793.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76664; AAC76664; b3640.
BAE77652; BAE77652; BAE77652.
GeneIDi12934430.
948607.
KEGGiecj:Y75_p3534.
eco:b3640.
PATRICi32122767. VBIEscCol129921_3760.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA30388. WPECDU.
RefSeqiNP_418097.1. NC_000913.3.
YP_491793.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
DisProtiDP00337.
ProteinModelPortaliP06968.
SMRiP06968. Positions 1-135.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP06968. 11 interactions.
MINTiMINT-1279301.
STRINGi511145.b3640.

2D gel databases

SWISS-2DPAGEP06968.

Proteomic databases

PaxDbiP06968.
PRIDEiP06968.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76664; AAC76664; b3640.
BAE77652; BAE77652; BAE77652.
GeneIDi12934430.
948607.
KEGGiecj:Y75_p3534.
eco:b3640.
PATRICi32122767. VBIEscCol129921_3760.

Organism-specific databases

EchoBASEiEB0247.
EcoGeneiEG10251. dut.

Phylogenomic databases

eggNOGiCOG0756.
HOGENOMiHOG000028968.
InParanoidiP06968.
KOiK01520.
OMAiILPRSGM.
OrthoDBiEOG689HXK.
PhylomeDBiP06968.

Enzyme and pathway databases

UniPathwayiUPA00610; UER00666.
BioCyciEcoCyc:DUTP-PYROP-MONOMER.
ECOL316407:JW3615-MONOMER.
MetaCyc:DUTP-PYROP-MONOMER.
BRENDAi3.6.1.23. 2026.

Miscellaneous databases

EvolutionaryTraceiP06968.
PROiP06968.

Gene expression databases

GenevestigatoriP06968.

Family and domain databases

Gene3Di2.70.40.10. 1 hit.
HAMAPiMF_00116. dUTPase_bact.
InterProiIPR029054. dUTPase-like.
IPR008180. dUTPase/dCTP_deaminase.
IPR008181. dUTPase_1.
[Graphical view]
PfamiPF00692. dUTPase. 1 hit.
[Graphical view]
SUPFAMiSSF51283. SSF51283. 1 hit.
TIGRFAMsiTIGR00576. dut. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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. 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. 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.

Entry informationi

Entry nameiDUT_ECOLI
AccessioniPrimary (citable) accession number: P06968
Secondary accession number(s): Q2M7V4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: April 1, 2015
This is version 146 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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.