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490  structures 8535  species 0  interactions 14635  sequences 179  architectures

Family: dUTPase (PF00692)

Summary: dUTPase

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This is the Wikipedia entry entitled "DUTP diphosphatase". More...

DUTP diphosphatase Edit Wikipedia article

dUTP diphosphatase
EC number3.6.1.23
CAS number37289-34-2
IntEnzIntEnz view
ExPASyNiceZyme view
MetaCycmetabolic pathway
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
PDB 1f7o EBI.jpg
crystal structures of feline immunodeficiency virus dutp pyrophosphatase and its nucleotide complexes in three crystal forms.
Pfam clanCL0153
PDB 1w2y EBI.jpg
the crystal structure of a complex of campylobacter jejuni dutpase with substrate analogue dupnhp
Pfam clanCL0231

In enzymology, a dUTP diphosphatase (EC 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]


  1. ^ 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.
  2. ^ Vassylyev DG, Morikawa K (1996). "Precluding uracil from DNA". Structure. 4 (12): 1381–5. doi:10.1016/S0969-2126(96)00145-1. PMID 8994964.
  3. ^ 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.
  4. ^ 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

This article incorporates text from the public domain Pfam and InterPro: IPR008180
This article incorporates text from the public domain Pfam and InterPro: IPR014871

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Literature references

  1. Cedergren-Zeppezauer ES, Larsson G, Nyman PO, Dauter Z, Wilson KS; , Nature 1992;355:740-743.: Crystal structure of a dUTPase. PUBMED:1311056 EPMC:1311056

  2. 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 ].

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

This family is a member of clan dUTPase (CL0153), which has the following description:

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 and the UniProtKB sequence database. More...

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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...


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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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 View help on the curation process

Seed source: Pfam-B_127 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 18
Number in full: 14635
Average length of the domain: 123.10 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 67.55 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 129
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 490 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
A0A0G2KN51 View 3D Structure Click here
A0A0R0GPR8 View 3D Structure Click here
A0A1D6KYW8 View 3D Structure Click here
A0A2R8QPR3 View 3D Structure Click here
A0KEM6 View 3D Structure Click here
A0KKF9 View 3D Structure Click here
A0Q1N5 View 3D Structure Click here
A0QQ98 View 3D Structure Click here
A0QW08 View 3D Structure Click here
A1A3S8 View 3D Structure Click here
A1BEP9 View 3D Structure Click here
A1K4K1 View 3D Structure Click here
A1KAG0 View 3D Structure Click here
A1RAW1 View 3D Structure Click here
A1S2D0 View 3D Structure Click here
A1S795 View 3D Structure Click here
A1SQ24 View 3D Structure Click here
A1SR17 View 3D Structure Click here
A1SSZ3 View 3D Structure Click here
A1T2M8 View 3D Structure Click here
A1T7Y0 View 3D Structure Click here
A1TL98 View 3D Structure Click here
A1U9Z8 View 3D Structure Click here
A1UF27 View 3D Structure Click here
A1URB3 View 3D Structure Click here
A1W538 View 3D Structure Click here
A1WUY3 View 3D Structure Click here
A1WZE9 View 3D Structure Click here
A2BLY5 View 3D Structure Click here
A2SIY4 View 3D Structure Click here
A2SQW1 View 3D Structure Click here
A3DFH7 View 3D Structure Click here
A3DNG5 View 3D Structure Click here
A3N3Q6 View 3D Structure Click here
A3QD95 View 3D Structure Click here
A3QIQ1 View 3D Structure Click here
A4G3E3 View 3D Structure Click here
A4G422 View 3D Structure Click here
A4SFI9 View 3D Structure Click here
A4VGS6 View 3D Structure Click here