This is the Wikipedia entry entitled "DUTP diphosphatase". More...
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DUTP diphosphatase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
crystal structures of feline immunodeficiency virus dutp pyrophosphatase and its nucleotide complexes in three crystal forms.
the crystal structure of a complex of campylobacter jejuni dutpase with substrate analogue dupnhp
- dUTP + H2O dUMP + diphosphate
This enzyme belongs to the family of hydrolases, specifically those acting on acid anhydrides in phosphorus-containing anhydrides. The systematic name of this enzyme class is dUTP nucleotidohydrolase. Other names in common use include deoxyuridine-triphosphatase, dUTPase, dUTP pyrophosphatase, desoxyuridine 5'-triphosphate nucleotidohydrolase, and desoxyuridine 5'-triphosphatase. This enzyme participates in pyrimidine metabolism.
This enzyme has a dual function: on one hand, it removes dUTP from the deoxynucleotide pool, which reduces the probability of this base being incorporated into DNA by DNA polymerases, while on the other hand, it produces the dTTP precursor dUMP. Lack or inhibition of dUTPase action leads to harmful perturbations in the nucleotide pool resulting in increased uracil content of DNA that activates a hyperactive futile cycle of DNA repair.
As of late 2007, 48 structures have been solved for this class of enzymes, with PDB accession codes 1DUC, 1DUD, 1DUN, 1DUP, 1DUT, 1EU5, 1EUW, 1F7D, 1F7K, 1F7N, 1F7O, 1F7P, 1F7Q, 1F7R, 1MQ7, 1OGH, 1OGK, 1OGL, 1PKH, 1PKJ, 1PKK, 1RN8, 1RNJ, 1SEH, 1SIX, 1SJN, 1SLH, 1SM8, 1SMC, 1SNF, 1SYL, 1VYQ, 1W2Y, 2BSY, 2BT1, 2CJE, 2D4L, 2D4M, 2D4N, 2HQU, 2HR6, 2HRM, 2OKB, 2OKD, 2OKE, 2OL0, 2OL1, and 2PY4.
There are at least two structurally distinct families of dUTPases. The crystal structure of human dUTPase reveals that each subunit of the dUTPase trimer folds into an eight-stranded jelly-roll beta barrel, with the C-terminal beta strands interchanged among the subunits. The structure is similar to that of the Escherichia coli enzyme, despite low sequence homology between the two enzymes.
- Vertessy BG, Toth J (2009). "Keeping uracil out of DNA". Accounts of Chemical Research 42 (1): 97–106. doi:10.1021/ar800114w. PMC 2732909. PMID 18837522.
- Vassylyev DG, Morikawa K (1996). "Precluding uracil from DNA". Structure 4 (12): 1381–5. doi:10.1016/S0969-2126(96)00145-1. PMID 8994964.
- Mol CD, Harris JM, McIntosh EM, Tainer JA (September 1996). "Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits". Structure 4 (9): 1077–92. doi:10.1016/S0969-2126(96)00114-1. PMID 8805593.
- Moroz, O. V.; Harkiolaki, M.; Galperin, M. Y.; Vagin, A. A.; González-Pacanowska, D.; Wilson, K. S. (2004). "The Crystal Structure of a Complex of Campylobacter jejuni dUTPase with Substrate Analogue Sheds Light on the Mechanism and Suggests the "Basic Module" for Dimeric d(C/U)TPases". Journal of Molecular Biology 342 (5): 1583–1597. doi:10.1016/j.jmb.2004.07.050. PMID 15364583.
- Bertani Le., Haeggmark A., Reichard P. (1963). "Enzymatic Synthesis of Deoxyribonucleotides. II. Formation and Interconversion of Deoxyuridine Phosphates". J. Biol. Chem. 238: 3407–13. PMID 14085395.
- Giroir LE, Deutsch WA (1987). "Drosophila deoxyuridine triphosphatase. Purification and characterization". J. Biol. Chem. 262 (1): 130–4. PMID 3025197.
- Greenberg Gr., Somerville Rl. (1962). "DEOXYURIDYLATE KINASE ACTIVITY AND DEOXYURIDINETRIPHOSPHATASE IN ESCHERICHIA COLI". Proc. Natl. Acad. Sci. U.S.A. 48 (2): 247–57. doi:10.1073/pnas.48.2.247. PMC 220766. PMID 13901467.
- Grindey GR, Nichol CA (1971). "Mammalian deoxyuridine 5'-triphosphate pyrophosphatase". Biochim. Biophys. Acta. 240 (2): 180–3. doi:10.1016/0005-2787(71)90655-1. PMID 5105331.
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dUTPase hydrolyses dUTP to dUMP and pyrophosphate.
Mol CD, Harris JM, McIntosh EM, Tainer JA; , Structure 1996;4:1077-1092.: Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. PUBMED:8805593 EPMC:8805593
Internal database links
|SCOOP:||HupF_HypC FTR Herpes_ORF11 Herpes_UL82_83 DCD AlgF DUF4353|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR008180
The essential enzyme deoxyuridine triphosphate nucleotidohydrolase (dUTPase) (EC) is specific for dUTP and is critical for the fidelity of DNA replication and repair. dUTPase hydrolyzes dUTP to dUMP and pyrophosphate, simultaneously reducing dUTP levels and providing the dUMP for dTTP biosynthesis. dUTPase decreases the intracellular concentration of dUPT so that uracil cannot be incorporated into DNA [PUBMED:8805593].
The crystal structure of human dUTPase reveals that each subunit of the dUTPase trimer folds into an eight-stranded jelly-roll beta barrel, with the C-terminal beta strands interchanged among the subunits. The structure is similar to that of the Escherichia coli enzyme, despite low sequence homology between the two enzymes [PUBMED:8805593].
Other enzymes like deoxycytidine triphosphate deaminase (dCTP) (EC) that specifically bind uridine also belong to this group suggesting that the signature may recognise a putative uridine-binding motif.
Some retroviruses encode dUTPases. Retroviral dUTPase is synthesised as part of POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, dUTPase and RNase H.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hydrolase activity (GO:0016787)|
|Biological process||dUTP metabolic process (GO:0046080)|
- the number of sequences which exhibit this architecture
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This clan contains dUTPase and many viral proteins that appear to be related. dUTPases are important in virus replication.
The clan contains the following 6 members:Cytomega_UL84 DCD dUTPase Herpes_ORF11 Herpes_U55 Herpes_UL82_83
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Curation and family details
|Seed source:||Pfam-B_127 (release 2.1)|
|Number in seed:||18|
|Number in full:||31922|
|Average length of the domain:||114.90 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||72.87 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the dUTPase domain has been found. There are 382 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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