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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 . 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.; 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 . 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
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
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR029054
This entry represents a distorted barrel domain found in deoxyuridine triphosphate nucleotidohydrolases and CTP deaminases.
Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) cleaves dUTP into pyrophosphate and dUMP. Three different subunit organisations of dUTPases have been found: they are either monomers, dimers or trimers [PUBMED:11375495]. dUTPases from E. coli [PUBMED:8646539], human [PUBMED:8805593], and some virus [PUBMED:9878436] all share a common distorted barrel fold and form trimers [PUBMED:15276840]. In the homotrimer, each subunit folds into a twisted antiparallel beta-barrel with the N and C-terminal portions interacting with adjacent subunits [PUBMED:9878436].
CTP deaminase is a member of the family of the structurally related trimeric dUTPases and the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii [PUBMED:15539408].
The monomeric dUTPase from Epstein-Barr virus mimics trimeric dUTPases. It consists of three domain, domains I and II having a dUTPase fold [PUBMED:16154087].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
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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 7 members:Cytomega_UL84 DCD dUTPase Herpes_ORF11 Herpes_U55 Herpes_UL82_83 TLP-20
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
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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.
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|Seed source:||Pfam-B_127 (release 2.1)|
|Number in seed:||18|
|Number in full:||12710|
|Average length of the domain:||123.60 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||71.63 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 432 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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