Summary: dUTPase
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This is the Wikipedia entry entitled "DUTP diphosphatase". More...
DUTP diphosphatase Edit Wikipedia article
| dUTP diphosphatase | |||||||||
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| Identifiers | |||||||||
| EC number | 3.6.1.23 | ||||||||
| CAS number | 37289-34-2 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
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| dUTPase | |||||||||
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 crystal structures of feline immunodeficiency virus dutp pyrophosphatase and its nucleotide complexes in three crystal forms. | |||||||||
| Identifiers | |||||||||
| Symbol | dUTPase | ||||||||
| Pfam | PF00692 | ||||||||
| Pfam clan | CL0153 | ||||||||
| InterPro | IPR008180 | ||||||||
| SCOPe | 1dup / SUPFAM | ||||||||
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| dUTPase_2 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 the crystal structure of a complex of campylobacter jejuni dutpase with substrate analogue dupnhp | |||||||||
| Identifiers | |||||||||
| Symbol | dUTPase_2 | ||||||||
| Pfam | PF08761 | ||||||||
| Pfam clan | CL0231 | ||||||||
| InterPro | IPR014871 | ||||||||
| SCOPe | 1w2y / SUPFAM | ||||||||
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In enzymology, a dUTP diphosphatase (EC 3.6.1.23) is an enzyme that catalyzes the chemical reaction
- dUTP + H2O dUMP + diphosphate
Thus, the two substrates of this enzyme are dUTP and H2O, whereas its two products are dUMP and 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.[1][2]
Structural studies
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.[3]
The second family has a novel all-alpha fold, members of this family are unrelated to the all-beta fold found in dUTPases of the majority of organisms.[4]
References
- ^ 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.
Further reading
- Bertani Le.; Haeggmark A.; Reichard P.; Interconversion of Deoxyuridine Phosphates (1963). "Enzymatic Synthesis of Deoxyribonucleotides. II. Formation". 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 G, Somerville R (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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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
dUTPase Provide feedback
2-Deoxyuridine 5-triphosphate nucleotidohydrolase (dUTPase) catalyses the hydrolysis of dUTP to dUMP and pyrophosphate ( EC:3.6.1.23). Members of this family have a novel all-alpha fold and are unrelated to the all-beta fold found in dUTPases of the majority of organisms [1]. This family contains both dUTPase homologues of dUTPase including dCTPase of phage T4.
Literature references
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Moroz OV, Harkiolaki M, Galperin MY, Vagin AA, Gonzalez-Pacanowska D, Wilson KS;, J Mol Biol. 2004;342:1583-1597.: 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. PUBMED:15364583 EPMC:15364583
Internal database links
| SCOOP: | MazG MazG-like PRA-PH |
External database links
| SCOP: | 1w2y |
This tab holds annotation information from the InterPro database.
InterPro entry IPR014871
This entry represents dimeric deoxyuridine triphosphate nucleotidohydrolase (dUTPase) ( EC ) and phage T4 dCTP pyrophosphatase ( EC ). dUTPase catalyses the hydrolysis of dUTP to dUMP and pyrophosphate. There are several classes of dUTPases: trimeric dUTPases found in most organisms and homologous monomeric dUTPases, found in mammalian herpesviruses. The dUTPases in this entry belong to a third class of dUTPases that form a dimer in solution and are able to hydrolyse both dUTP and dUDP [ PUBMED:11420444 ]. It contains a novel all-alpha fold that is unrelated to the all-beta fold found in dUTPases of the majority of organisms [ PUBMED:15364583 ].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
Alignments
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| Seed (16) |
Full (1065) |
Representative proteomes | UniProt (5137) |
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| RP15 (283) |
RP35 (631) |
RP55 (1074) |
RP75 (1651) |
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| Jalview | |||||||
| HTML | |||||||
| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (16) |
Full (1065) |
Representative proteomes | UniProt (5137) |
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| RP15 (283) |
RP35 (631) |
RP55 (1074) |
RP75 (1651) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | pdb_1w2y |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Mistry J 
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| Number in seed: | 16 |
| Number in full: | 1065 |
| Average length of the domain: | 145.60 aa |
| Average identity of full alignment: | 25 % |
| Average coverage of the sequence by the domain: | 88.47 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 164 | ||||||||||||
| Family (HMM) version: | 13 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Structures
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_2 domain has been found. There are 34 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 sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
| Protein | Predicted structure | External Information |
|---|---|---|
| A4HSU8 | View 3D Structure | Click here |
| Q2FWS5 | View 3D Structure | Click here |
| Q4DI50 | View 3D Structure | Click here |
| Q4E2Y0 | View 3D Structure | Click here |
