Deoxyuridine 5'-triphosphate nucleotidohydrolase

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P06968 (DUT_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 129. 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) [Reference proteome] [HAMAP]

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-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 process	Nucleotide metabolism
Ligand	Magnesium Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	dUMP biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway dUTP metabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	cytosol Inferred from direct assay PubMed 16858726. Source: UniProtKB
Molecular_function	dUTP diphosphatase activity Inferred from direct assay PubMed 346589. Source: EcoCyc magnesium ion binding Inferred from electronic annotation. Source: HAMAP
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-Rule 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.10

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] [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 277:1453-1474(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.

PIR

WPECDU. A30388.

RefSeq

NP_418097.1. NC_000913.2.
YP_491793.1. NC_007779.1.

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	[»]

DisProt

DP00337.

ProteinModelPortal

P06968.

SMR

P06968. Positions 1-135.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9483N.

IntAct

P06968. 10 interactions.

MINT

MINT-1279301.

STRING

511145.b3640.

2D gel databases

SWISS-2DPAGE

P06968.

Proteomic databases

PaxDb

P06968.

PRIDE

P06968.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76664; AAC76664; b3640.
BAE77652; BAE77652; BAE77652.

GeneID

12934430.
948607.

KEGG

ecj:Y75_p3534.
eco:b3640.

PATRIC

32122767. VBIEscCol129921_3760.

Organism-specific databases

EchoBASE

EB0247.

EcoGene

EG10251. dut.

Phylogenomic databases

eggNOG

COG0756.

HOGENOM

HOG000028968.

K01520.

OMA

ILPRSGM.

ProtClustDB

PRK00601.

Enzyme and pathway databases

BioCyc

EcoCyc:DUTP-PYROP-MONOMER.
ECOL316407:JW3615-MONOMER.
MetaCyc:DUTP-PYROP-MONOMER.

UniPathway

UPA00610; UER00666.

Gene expression databases

Genevestigator

P06968.

Family and domain databases

HAMAP

MF_00116. dUTPase_bact.

InterPro

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

PANTHER

PTHR11241. PTHR11241. 1 hit.

Pfam

PF00692. dUTPase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00576. dut. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P06968.

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:	May 1, 2013
This is version 129 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

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents