Deoxyuridine 5'-triphosphate nucleotidohydrolase

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P06968 (DUT_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 117. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	151 AA.
Sequence status	Complete.
Protein existence	Evidence 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 MF_00116
Catalytic activity	dUTP + H₂O = dUMP + diphosphate. HAMAP MF_00116
Cofactor	Magnesium. Ref.9
Pathway	Pyrimidine metabolism; dUMP biosynthesis; dUMP from dCTP (dUTP route): step 2/2. HAMAP MF_00116
Subunit structure	Homotrimer. Ref.9
Sequence similarities	Belongs to the dUTPase family.

Ontologies

Keywords
Biological process	Nucleotide metabolism
Ligand	Magnesium Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	dUTP metabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytosol Inferred from direct assay. Source: UniProtKB
Molecular function	dUTP diphosphatase activity Inferred from direct assay. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 151

151

Deoxyuridine 5'-triphosphate nucleotidohydrolase HAMAP MF_00116

PRO_0000182858

Regions

Region

70 – 72

Substrate binding By similarity

Region

87 – 89

Substrate binding Probable

Sites

Binding site

Substrate

Binding site

Substrate; via amide nitrogen and carbonyl oxygen

Experimental info

Mutagenesis

D → N: Reduces catalytic activity 40000-fold. Ref.9

Secondary structure

151

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P06968 [UniParc].

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

151

16,155

        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' referencesShow '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: 6139280] [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: 7686882] [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 277:1453-1474(1997) [PubMed: 9278503] [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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"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: 1311056] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[6]	"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: 8646539] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[7]	"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: 9757088] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[8]	"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: 11375495] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS).
[9]	"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: 15208312] [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.

PIR

WPECDU. A30388.

RefSeq

NP_418097.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DUD	X-ray	2.30	A	1-151	[»]
1DUP	X-ray	1.90	A	1-151	[»]
1EU5	X-ray	1.45	A	1-151	[»]
1EUW	X-ray	1.05	A	1-151	[»]
1RN8	X-ray	1.93	A	1-151	[»]
1RNJ	X-ray	1.70	A	1-151	[»]
1SEH	X-ray	1.47	A	1-151	[»]
1SYL	X-ray	1.95	A	1-151	[»]
2HR6	X-ray	1.84	A	1-151	[»]
2HRM	X-ray	1.70	A	1-151	[»]

ProteinModelPortal

P06968.

SMR

P06968. Positions 1-135.

DisProt

DP00337.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9483N.

IntAct

P06968. 12 interactions.

MINT

MINT-1279301.

2D gel databases

SWISS-2DPAGE

P06968.

ECO2DBASE

C017.2. 6TH EDITION.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000002984; EBESCP00000002984; EBESCG00000002444.
EBESCT00000016134; EBESCP00000015425; EBESCG00000015194.

GeneID

948607.

GenomeReviews

Gene locus JW3615 in contig AP009048_GR.
Gene locus b3640 in contig U00096_GR.

KEGG

ecj:JW3615.
eco:b3640.

PATRIC

32122767. VBIEscCol129921_3760.

Organism-specific databases

EchoBASE

EB0247.

EcoGene

EG10251. dut.

Phylogenomic databases

eggNOG

COG0756.

GeneTree

EBGT00050000011819.

HOGENOM

HBG436079.

OMA

LDLRACI.

PhylomeDB

P06968.

ProtClustDB

PRK00601.

Enzyme and pathway databases

BioCyc

EcoCyc:DUTP-PYROP-MONOMER.
MetaCyc:DUTP-PYROP-MONOMER.

Gene expression databases

Genevestigator

P06968.

Family and domain databases

HAMAP

MF_00116. dUTPase_bact.
[Tree]

InterPro

IPR008180. dUTP_pyroPase.
IPR008181. dUTP_pyroPase_sf.
[Graphical view]

K01520.

PANTHER

PTHR11241. PTHR11241. 1 hit.

Pfam

PF00692. dUTPase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00576. Dut. 1 hit.

ProtoNet

Search...

Entry information

Entry name

DUT_ECOLI

Accession

Primary (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:	January 25, 2012
This is version 117 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents