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PDBsum entry 1q5h

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1q5h
Jmol
Contents
Protein chains
127 a.a. *
136 a.a. *
Ligands
DUD ×3
Metals
_MG
Waters ×238
* Residue conservation analysis
PDB id:
1q5h
Name: Hydrolase
Title: Human dutp pyrophosphatase complex with dudp
Structure: Dutp pyrophosphatase. Chain: a, b, c. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
Resolution:
2.00Å     R-factor:   0.179     R-free:   0.214
Authors: C.D.Mol,J.M.Harris,E.M.Mcintosh,J.A.Tainer
Key ref:
C.D.Mol et al. (1996). Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits. Structure, 4, 1077-1092. PubMed id: 8805593 DOI: 10.1016/S0969-2126(96)00114-1
Date:
07-Aug-03     Release date:   19-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P33316  (DUT_HUMAN) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
Seq:
Struc:
252 a.a.
127 a.a.
Protein chains
Pfam   ArchSchema ?
P33316  (DUT_HUMAN) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
Seq:
Struc:
252 a.a.
136 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.3.6.1.23  - dUTP diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: dUTP + H2O = dUMP + diphosphate
dUTP
Bound ligand (Het Group name = DUD)
matches with 85.71% similarity
+ H(2)O
= dUMP
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     dUTP metabolic process   1 term 
  Biochemical function     hydrolase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(96)00114-1 Structure 4:1077-1092 (1996)
PubMed id: 8805593  
 
 
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
C.D.Mol, J.M.Harris, E.M.McIntosh, J.A.Tainer.
 
  ABSTRACT  
 
BACKGROUND. The essential enzyme dUTP pyrophosphatase (dUTPase) is exquisitely 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. A high cellular dTTP: dUTP ratio is essential to avoid uracil incorporation into DNA, which would lead to strand breaks and cell death. We report the first detailed atomic-resolution structure of a eukaryotic dUTPase, human dUTPase, and complexes with the uracil-containing deoxyribonucleotides, dUMP, dUDP and dUTP. RESULTS. The crystal structure 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 E. coli enzyme, despite low sequence homology between the two enzymes. The nucleotide complexes reveal a simple and elegant way for a beta hairpin to recognize specific nucleic acids: uracil is inserted into a distorted antiparallel beta hairpin and hydrogen bonds entirely to main-chain atoms. This interaction mimics DNA base pairing, selecting uracil over cytosine and sterically precluding thymine and ribose binding. Residues from the second subunit interact with the phosphate groups and a glycine-rich C-terminal tail of the third subunit caps the substrate-bound active site, causing total complementary enclosure of substrate. To our knowledge, this is the first documented instance of all three subunits of a trimeric enzyme supplying residues that are critical to enzyme function and catalysis. CONCLUSIONS. The dUTPase nucleotide-binding sites incorporate some features of other nucleotide-binding proteins and protein kinases, but seem distinct in sequence and architecture. The novel nucleic acid base recognition motif appears ancient; higher order structures, such as the ribosome, may have evolved from a motif of this kind. These uracil-beta-hairpin interactions are an obvious way for peptides to become early coenzymes in an RNA world, providing a plausible link to the protein-DNA world. Within the beta hairpin, there is a tyrosine corner motif that normally specifies beta-arch connections; this tyrosine motif was apparently recruited to discriminate against ribonucleotides, more recently than the evolution of the beta hairpin itself.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. Schematic of dUTPase-substrate interactions showing the structural basis for the exquisite specificity for dUTP that requires all three subunits. Hydrogen bonds (<3.4 ) are shown (dashed lines) with the donor-acceptor atom distance beneath the protein atom label. Hydrophobic interactions (wavy lines) are shown only for the key residues Tyr82, which packs against the deoxyribose, and Phe135, which stacks above the bound uracil base. Uracil and deoxyribose are primarily recognized by one subunit (gold rectangles), phosphate groups by the adjacent subunit (purple rectangles), whereas the bound substrate is capped by residues from the C-terminal tail of a third subunit (blue rectangles).
 
  The above figure is reprinted by permission from Cell Press: Structure (1996, 4, 1077-1092) copyright 1996.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20705648 G.Sharbeen, A.J.Cook, K.K.Lau, J.Raftery, C.W.Yee, and C.J.Jolly (2010).
Incorporation of dUTP does not mediate mutation of A:T base pairs in Ig genes in vivo.
  Nucleic Acids Res, 38, 8120-8130.  
  20944217 G.W.Han, M.A.Elsliger, T.O.Yeates, Q.Xu, A.G.Murzin, S.S.Krishna, L.Jaroszewski, P.Abdubek, T.Astakhova, H.L.Axelrod, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, D.Ernst, J.Feuerhelm, J.C.Grant, A.Grzechnik, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, A.Kumar, W.W.Lam, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1237-1244.
PDB code: 3nl9
20601405 I.Pecsi, I.Leveles, V.Harmat, B.G.Vertessy, and J.Toth (2010).
Aromatic stacking between nucleobase and enzyme promotes phosphate ester hydrolysis in dUTPase.
  Nucleic Acids Res, 38, 7179-7186.
PDB codes: 3hza 3loj
20823546 J.García-Nafría, L.Burchell, M.Takezawa, N.J.Rzechorzek, M.J.Fogg, and K.S.Wilson (2010).
The structure of the genomic Bacillus subtilis dUTPase: novel features in the Phe-lid.
  Acta Crystallogr D Biol Crystallogr, 66, 953-961.
PDB codes: 2xcd 2xce
18837522 B.G.Vértessy, and J.Tóth (2009).
Keeping uracil out of DNA: physiological role, structure and catalytic mechanism of dUTPases.
  Acc Chem Res, 42, 97.  
  19342774 G.L.Li, J.Wang, L.F.Li, and X.D.Su (2009).
Crystallization and preliminary X-ray analysis of three dUTPases from Gram-positive bacteria.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 339-342.  
  19851015 K.Homma, and H.Moriyama (2009).
Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 1030-1034.
PDB codes: 3c2t 3c3i 3ca9
19586911 L.Freeman, M.Buisson, N.Tarbouriech, A.Van der Heyden, P.Labbé, and W.P.Burmeister (2009).
The flexible motif V of Epstein-Barr virus deoxyuridine 5'-triphosphate pyrophosphatase is essential for catalysis.
  J Biol Chem, 284, 25280-25289.
PDB codes: 2we0 2we1 2we2 2we3
19015155 P.M.Wilson, W.Fazzone, M.J.LaBonte, H.J.Lenz, and R.D.Ladner (2009).
Regulation of human dUTPase gene expression and p53-mediated transcriptional repression in response to oxaliplatin-induced DNA damage.
  Nucleic Acids Res, 37, 78-95.  
17932923 J.Kovári, O.Barabás, B.Varga, A.Békési, F.Tölgyesi, J.Fidy, J.Nagy, and B.G.Vértessy (2008).
Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
  Proteins, 71, 308-319.
PDB codes: 2hr6 2hrm
18790783 P.M.Wilson, W.Fazzone, M.J.LaBonte, J.Deng, N.Neamati, and R.D.Ladner (2008).
Novel opportunities for thymidylate metabolism as a therapeutic target.
  Mol Cancer Ther, 7, 3029-3037.  
19029943 R.T.Javier (2008).
Cell polarity proteins: common targets for tumorigenic human viruses.
  Oncogene, 27, 7031-7046.  
17828302 S.H.Chung, R.S.Weiss, K.K.Frese, B.V.Prasad, and R.T.Javier (2008).
Functionally distinct monomers and trimers produced by a viral oncoprotein.
  Oncogene, 27, 1412-1420.  
17452782 A.Samal, N.Schormann, W.J.Cook, L.J.DeLucas, and D.Chattopadhyay (2007).
Structures of vaccinia virus dUTPase and its nucleotide complexes.
  Acta Crystallogr D Biol Crystallogr, 63, 571-580.
PDB codes: 2okb 2okd 2oke 2ol0 2ol1
17848562 J.Tóth, B.Varga, M.Kovács, A.Málnási-Csizmadia, and B.G.Vértessy (2007).
Kinetic mechanism of human dUTPase, an essential nucleotide pyrophosphatase enzyme.
  J Biol Chem, 282, 33572-33582.  
  17565183 M.Bajaj, and H.Moriyama (2007).
Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 409-411.
PDB code: 2pc5
17314165 S.H.Chung, K.K.Frese, R.S.Weiss, B.V.Prasad, and R.T.Javier (2007).
A new crucial protein interaction element that targets the adenovirus E4-ORF1 oncoprotein to membrane vesicles.
  J Virol, 81, 4787-4797.  
17169987 V.Németh-Pongrácz, O.Barabás, M.Fuxreiter, I.Simon, I.Pichová, M.Rumlová, H.Zábranská, D.Svergun, M.Petoukhov, V.Harmat, E.Klement, E.Hunyadi-Gulyás, K.F.Medzihradszky, E.Kónya, and B.G.Vértessy (2007).
Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.
  Nucleic Acids Res, 35, 495-505.
PDB codes: 2d4l 2d4m 2d4n
17549447 Y.Cho, H.S.Lee, Y.J.Kim, S.G.Kang, S.J.Kim, and J.H.Lee (2007).
Characterization of a dUTPase from the hyperthermophilic archaeon Thermococcus onnurineus NA1 and its application in polymerase chain reaction amplification.
  Mar Biotechnol (NY), 9, 450-458.  
16188990 A.J.Davison, and N.D.Stow (2005).
New genes from old: redeployment of dUTPase by herpesviruses.
  J Virol, 79, 12880-12892.  
15539408 E.Johansson, M.Fanø, J.H.Bynck, J.Neuhard, S.Larsen, B.W.Sigurskjold, U.Christensen, and M.Willemoës (2005).
Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes.
  J Biol Chem, 280, 3051-3059.
PDB codes: 1xs1 1xs4 1xs6
15698576 J.L.Whittingham, I.Leal, C.Nguyen, G.Kasinathan, E.Bell, A.F.Jones, C.Berry, A.Benito, J.P.Turkenburg, E.J.Dodson, L.M.Ruiz Perez, A.J.Wilkinson, N.G.Johansson, R.Brun, I.H.Gilbert, D.Gonzalez Pacanowska, and K.S.Wilson (2005).
dUTPase as a platform for antimalarial drug design: structural basis for the selectivity of a class of nucleoside inhibitors.
  Structure, 13, 329-338.
PDB code: 1vyq
16154087 N.Tarbouriech, M.Buisson, J.M.Seigneurin, S.Cusack, and W.P.Burmeister (2005).
The monomeric dUTPase from Epstein-Barr virus mimics trimeric dUTPases.
  Structure, 13, 1299-1310.
PDB codes: 2bsy 2bt1
16014955 Y.Zhang, H.Moriyama, K.Homma, and J.L.Van Etten (2005).
Chlorella virus-encoded deoxyuridine triphosphatases exhibit different temperature optima.
  J Virol, 79, 9945-9953.  
15459796 J.Abe, T.Kubo, Y.Takagi, T.Saito, K.Miura, H.Fukuzawa, and Y.Matsuda (2004).
The transcriptional program of synchronous gametogenesis in Chlamydomonas reinhardtii.
  Curr Genet, 46, 304-315.  
14724274 J.Kovári, O.Barabás, E.Takács, A.Békési, Z.Dubrovay, V.Pongrácz, I.Zagyva, T.Imre, P.Szabó, and B.G.Vértessy (2004).
Altered active site flexibility and a structural metal-binding site in eukaryotic dUTPase: kinetic characterization, folding, and crystallographic studies of the homotrimeric Drosophila enzyme.
  J Biol Chem, 279, 17932-17944.  
15146494 L.M.Iyer, and L.Aravind (2004).
The emergence of catalytic and structural diversity within the beta-clip fold.
  Proteins, 55, 977-991.  
14725764 M.Harkiolaki, E.J.Dodson, V.Bernier-Villamor, J.P.Turkenburg, D.González-Pacanowska, and K.S.Wilson (2004).
The crystal structure of Trypanosoma cruzi dUTPase reveals a novel dUTP/dUDP binding fold.
  Structure, 12, 41-53.
PDB codes: 1ogk 1ogl
15208312 O.Barabás, V.Pongrácz, J.Kovári, M.Wilmanns, and B.G.Vértessy (2004).
Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
  J Biol Chem, 279, 42907-42915.
PDB codes: 1rn8 1rnj 1seh 1syl
14724273 Z.Dubrovay, Z.Gáspári, E.Hunyadi-Gulyás, K.F.Medzihradszky, A.Perczel, and B.G.Vértessy (2004).
Multidimensional NMR identifies the conformational shift essential for catalytic competence in the 60-kDa Drosophila melanogaster dUTPase trimer.
  J Biol Chem, 279, 17945-17950.  
12721364 D.Mustafi, A.Bekesi, B.G.Vertessy, and M.W.Makinen (2003).
Catalytic and structural role of the metal ion in dUTP pyrophosphatase.
  Proc Natl Acad Sci U S A, 100, 5670-5675.  
12756253 E.Johansson, O.Bjornberg, P.O.Nyman, and S.Larsen (2003).
Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii and its relation to other homotrimeric dUTPases.
  J Biol Chem, 278, 27916-27922.
PDB code: 1ogh
12538648 H.Li, H.Xu, D.E.Graham, and R.H.White (2003).
The Methanococcus jannaschii dCTP deaminase is a bifunctional deaminase and diphosphatase.
  J Biol Chem, 278, 11100-11106.  
12869552 O.Barabás, M.Rumlová, A.Erdei, V.Pongrácz, I.Pichová, and B.G.Vértessy (2003).
dUTPase and nucleocapsid polypeptides of the Mason-Pfizer monkey virus form a fusion protein in the virion with homotrimeric organization and low catalytic efficiency.
  J Biol Chem, 278, 38803-38812.  
12670946 O.Björnberg, J.Neuhard, and P.O.Nyman (2003).
A bifunctional dCTP deaminase-dUTP nucleotidohydrolase from the hyperthermophilic archaeon Methanocaldococcus jannaschii.
  J Biol Chem, 278, 20667-20672.  
11375495 A.González, G.Larsson, R.Persson, and E.Cedergren-Zeppezauer (2001).
Atomic resolution structure of Escherichia coli dUTPase determined ab initio.
  Acta Crystallogr D Biol Crystallogr, 57, 767-774.
PDB codes: 1eu5 1euw
11468401 B.W.Han, J.Y.Lee, J.K.Yang, B.I.Lee, and S.W.Suh (2001).
Crystallization and preliminary X-ray crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Saccharomyces cerevisiae.
  Acta Crystallogr D Biol Crystallogr, 57, 1147-1149.  
11420444 F.Hidalgo-Zarco, A.G.Camacho, V.Bernier-Villamor, J.Nord, L.M.Ruiz-Pérez, and D.González-Pacanowska (2001).
Kinetic properties and inhibition of the dimeric dUTPase-dUDPase from Leishmania major.
  Protein Sci, 10, 1426-1433.  
11320329 K.M.Kim, E.C.Yi, D.Baker, and K.Y.Zhang (2001).
Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase.
  Acta Crystallogr D Biol Crystallogr, 57, 759-762.  
11533155 K.Reus, J.Mayer, M.Sauter, H.Zischler, N.Müller-Lantzsch, and E.Meese (2001).
HERV-K(OLD): ancestor sequences of the human endogenous retrovirus family HERV-K(HML-2).
  J Virol, 75, 8917-8926.  
11375514 R.Persson, M.Harkiolaki, J.McGeehan, and K.S.Wilson (2001).
Crystallization and preliminary crystallographic analysis of deoxyuridine 5'-triphosphate nucleotidohydrolase from Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 57, 876-878.  
10957629 G.S.Prasad, E.A.Stura, J.H.Elder, and C.D.Stout (2000).
Structures of feline immunodeficiency virus dUTP pyrophosphatase and its nucleotide complexes in three crystal forms.
  Acta Crystallogr D Biol Crystallogr, 56, 1100-1109.
PDB codes: 1f7d 1f7k 1f7n 1f7o 1f7p 1f7q 1f7r
  10438861 A.M.Baldo, and M.A.McClure (1999).
Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts.
  J Virol, 73, 7710-7721.  
  10515998 M.Oliveros, R.García-Escudero, A.Alejo, E.Viñuela, M.L.Salas, and J.Salas (1999).
African swine fever virus dUTPase is a highly specific enzyme required for efficient replication in swine macrophages.
  J Virol, 73, 8934-8943.  
10089367 V.Bernier-Villamor, A.Camacho, D.González-Pacanowska, E.Cedergren-Zeppezauer, A.Antson, and K.S.Wilson (1999).
Crystallization and preliminary X-ray diffraction of Trypanosoma cruzi dUTPase.
  Acta Crystallogr D Biol Crystallogr, 55, 528-530.  
9497317 D.Prangishvili, H.P.Klenk, G.Jakobs, A.Schmiechen, C.Hanselmann, I.Holz, and W.Zillig (1998).
Biochemical and phylogenetic characterization of the dUTPase from the archaeal virus SIRV.
  J Biol Chem, 273, 6024-6029.  
9083108 M.Bergdoll, M.H.Remy, C.Cagnon, J.M.Masson, and P.Dumas (1997).
Proline-dependent oligomerization with arm exchange.
  Structure, 5, 391-401.  
9228092 R.D.Ladner, and S.J.Caradonna (1997).
The human dUTPase gene encodes both nuclear and mitochondrial isoforms. Differential expression of the isoforms and characterization of a cDNA encoding the mitochondrial species.
  J Biol Chem, 272, 19072-19080.  
8994964 D.G.Vassylyev, and K.Morikawa (1996).
Precluding uracil from DNA.
  Structure, 4, 1381-1385.  
  8976551 G.S.Prasad, E.A.Stura, D.E.McRee, G.S.Laco, C.Hasselkus-Light, J.H.Elder, and C.D.Stout (1996).
Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus.
  Protein Sci, 5, 2429-2437.
PDB code: 1dut
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.