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PDBsum entry 2bsy

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protein ligands links
Hydrolase PDB id
2bsy
Jmol
Contents
Protein chain
249 a.a. *
Ligands
UMP
SO4 ×4
Waters ×305
* Residue conservation analysis
PDB id:
2bsy
Name: Hydrolase
Title: Epstein barr virus dutpase
Structure: Deoxyuridine 5'-triphosphate nucleotidohydrolase. Chain: a. Synonym: dutpase, dutp pyrophosphatase. Engineered: yes
Source: Human herpesvirus 4. Epstein-barr virus. Organism_taxid: 10376. Strain: b95-8. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.50Å     R-factor:   0.150     R-free:   0.187
Authors: N.Tarbouriech,M.Buisson,J.-M. Seigneurin,S.Cusack, W.P.Burmeister
Key ref:
N.Tarbouriech et al. (2005). The monomeric dUTPase from Epstein-Barr virus mimics trimeric dUTPases. Structure, 13, 1299-1310. PubMed id: 16154087 DOI: 10.1016/j.str.2005.06.009
Date:
24-May-05     Release date:   15-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P03195  (DUT_EBVB9) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase
Seq:
Struc:
278 a.a.
249 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.23  - dUTP diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: dUTP + H2O = dUMP + diphosphate
dUTP
+ H(2)O
=
dUMP
Bound ligand (Het Group name = UMP)
corresponds exactly
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleotide metabolic process   2 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2005.06.009 Structure 13:1299-1310 (2005)
PubMed id: 16154087  
 
 
The monomeric dUTPase from Epstein-Barr virus mimics trimeric dUTPases.
N.Tarbouriech, M.Buisson, J.M.Seigneurin, S.Cusack, W.P.Burmeister.
 
  ABSTRACT  
 
Deoxyuridine 5'-triphosphate pyrophosphatases (dUTPases) are ubiquitous enzymes cleaving dUTP into dUMP and pyrophosphate. They occur as monomeric, dimeric, or trimeric molecules. The trimeric and monomeric enzymes both contain the same five characteristic sequence motifs but in a different order, whereas the dimeric enzymes are not homologous. Monomeric dUTPases only occur in herpesviruses, such as Epstein-Barr virus (EBV). Here, we describe the crystal structures of EBV dUTPase in complex with the product dUMP and a substrate analog alpha,beta-imino-dUTP. The molecule consists of three domains forming one active site that has a structure extremely similar to one of the three active sites of trimeric dUTPases. The three domains functionally correspond to the subunits of the trimeric form. Domains I and II have the dUTPase fold, but they differ considerably in the regions that are not involved in the formation of the unique active site, whereas domain III has only little secondary structure.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Superposition of the Two dUTPase-like Domains of EBV dUTPase
Stereoview in which domain I is colored in green and domain II is in red. The superposition used the CCP4MG software. Secondary structure elements are labeled according to Figure 1C, with N or C specified if the element is specific for domains I or II.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1299-1310) copyright 2005.  
  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
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.  
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
17554050 K.L.Maxwell, and L.Frappier (2007).
Viral proteomics.
  Microbiol Mol Biol Rev, 71, 398-411.  
16650981 A.Andreeva, and A.G.Murzin (2006).
Evolution of protein fold in the presence of functional constraints.
  Curr Opin Struct Biol, 16, 399-408.  
17001096 M.J.Fogg, P.Alzari, M.Bahar, I.Bertini, J.M.Betton, W.P.Burmeister, C.Cambillau, B.Canard, M.A.Corrondo, M.Carrondo, M.Coll, S.Daenke, O.Dym, M.P.Egloff, F.J.Enguita, A.Geerlof, A.Haouz, T.A.Jones, Q.Ma, S.N.Manicka, M.Migliardi, P.Nordlund, R.J.Owens, Y.Peleg, G.Schneider, R.Schnell, D.I.Stuart, N.Tarbouriech, T.Unge, A.J.Wilkinson, M.Wilmanns, K.S.Wilson, O.Zimhony, and J.M.Grimes (2006).
Application of the use of high-throughput technologies to the determination of protein structures of bacterial and viral pathogens.
  Acta Crystallogr D Biol Crystallogr, 62, 1196-1207.  
17001105 N.Tarbouriech, M.Buisson, T.Géoui, S.Daenke, S.Cusack, and W.P.Burmeister (2006).
Structural genomics of the Epstein-Barr virus.
  Acta Crystallogr D Biol Crystallogr, 62, 1276-1285.  
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.