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PDBsum entry 1dun

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protein links
Hydrolase PDB id
1dun
Jmol
Contents
Protein chain
120 a.a. *
Waters ×133
* Residue conservation analysis
PDB id:
1dun
Name: Hydrolase
Title: Eiav dutpase native
Structure: Deoxyuridine 5'-triphosphate nucleoditohydrolase. Chain: a. Synonym: dutpase, dutp pyrophosphatase. Engineered: yes
Source: Equine infectious anemia virus. Organism_taxid: 11665. Cell_line: bl21. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.159     R-free:   0.215
Authors: Z.Dauter,R.Persson,A.M.Rosengren,P.O.Nyman,K.S.Wilson, E.S.Cedergren-Zeppezauer
Key ref:
Z.Dauter et al. (1999). Crystal structure of dUTPase from equine infectious anaemia virus; active site metal binding in a substrate analogue complex. J Mol Biol, 285, 655-673. PubMed id: 9878436 DOI: 10.1006/jmbi.1998.2332
Date:
27-Nov-97     Release date:   27-May-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11204  (POL_EIAV9) -  Pol polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1146 a.a.
120 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.2.7.7.49  - RNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
   Enzyme class 3: E.C.3.1.13.2  - Exoribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
   Enzyme class 4: E.C.3.1.26.13  - Retroviral ribonuclease H.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
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     1 term  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1998.2332 J Mol Biol 285:655-673 (1999)
PubMed id: 9878436  
 
 
Crystal structure of dUTPase from equine infectious anaemia virus; active site metal binding in a substrate analogue complex.
Z.Dauter, R.Persson, A.M.Rosengren, P.O.Nyman, K.S.Wilson, E.S.Cedergren-Zeppezauer.
 
  ABSTRACT  
 
The X-ray structures of dUTPase from equine infectious anaemia virus (EIAV) in unliganded and complexed forms have been determined to 1.9 and 2.0 A resolution, respectively. The structures were solved by molecular replacement using Escherichia coli dUTPase as search model. The exploitation of a relatively novel refinement approach for the initial model, combining maximum likelihood refinement with stereochemically unrestrained updating of the model, proved to be of crucial importance and should be of general relevance.EIAV dUTPase is a homotrimer where each subunit folds into a twisted antiparallel beta-barrel with the N and C-terminal portions interacting with adjacent subunits. The C-terminal 14 and 17 amino acid residues are disordered in the crystal structure of the unliganded and complexed enzyme, respectively. Interactions along the 3-fold axis include a water-containing volume (size 207 A3) which has no contact with bulk solvent.It has earlier been shown that a divalent metal ion is essential for catalysis. For the first time, a putative binding site for such a metal ion, in this case Sr2+, is established. The positions of the inhibitor (the non-hydrolysable substrate analogue dUDP) and the metal ion in the complex are consistent with the location of the active centre established for trimeric dUTPase structures, in which subunit interfaces form three surface clefts lined with evolutionary conserved residues. However, a detailed comparison of the active sites of the EIAV and E. coli enzymes reveals some structural differences. The viral enzyme undergoes a small conformational change in the uracil-binding beta-hairpin structure upon dUDP binding not observed in the other known dUTPase structures.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo views of the electron density around the active site. (a) Unliganded EIAV dUTPase contoured at 1.2 σ showing the peptide Asn-Gly-Gly-Ile with the bond of Gly68-Gly69 in two alternative conformations (A and B) related by a peptide flip. (b) The Gly68-Gly69 peptide has a single, well-ordered orientation (B) in the complex contoured at 2 σ. (c) dUDP and Sr^2+(grey) with its six water ligands bound (red), again contoured at 2 σ. The bonds between the metal ion and the oxygen atoms of the α and β-phosphates are 2.47 Å and 2.69 Å, respectively. The bond lengths between the Sr^2+ and its water ligands range between 2.77 Å and 2.85 Å. Figures generated using QUANTA.
Figure 5.
Figure 5. Superposition (based on the alignment of 53 CA atoms described in Figure 3) of the backbones of unliganded dUTPases from EIAV (blue), FIV (green), E. coli (red) and human (yellow), viewed down the 3-fold axis. (a) Monomers. Every tenth residue of EIAV dUTPase is numbered. (b) Trimers. 159 CA atoms were superimposed. Figures were generated using MOLSCRIPT [Kraulis 1991].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 655-673) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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
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
20461535 J.Gong, Y.H.Huang, X.H.Huang, R.Zhang, and Q.W.Qin (2010).
Nuclear-export-signal-dependent protein translocation of dUTPase encoded by Singapore grouper iridovirus.
  Arch Virol, 155, 1069-1076.  
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.  
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
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
18646465 L.C.Zhao, A.C.Cheng, M.S.Wang, G.P.Yuan, R.Y.Jia, D.C.Zhou, X.F.Qi, H.Ge, and T.Sun (2008).
Identification and characterization of duck enteritis virus dUTPase gene.
  Avian Dis, 52, 324-331.  
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
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.  
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.  
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.  
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
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
11567158 A.Perrakis, M.Harkiolaki, K.S.Wilson, and V.S.Lamzin (2001).
ARP/wARP and molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 57, 1445-1450.  
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.  
11375528 M.Harkiolaki, A.M.Brzozowski, D.Gonzalez-Pacanowska, F.Hidalgo-Zarco, and K.S.Wilson (2001).
New crystal forms of Trypanosoma cruzi dUTPase.
  Acta Crystallogr D Biol Crystallogr, 57, 915-917.  
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.  
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.