PDBsum entry 2hr6

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Hydrolase PDB id
Protein chain
137 a.a. *
Waters ×156
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of dutpase in complex with substrate analo and manganese
Structure: Deoxyuridine 5'-triphosphate nucleotidohydrolase. Chain: a. Synonym: dutpase, dutp pyrophosphatase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: dut. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.84Å     R-factor:   0.152     R-free:   0.173
Authors: O.Barabas,J.Kovari,R.Tapai,B.G.Vertessy
Key ref:
J.Kovári et al. (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. PubMed id: 17932923 DOI: 10.1002/prot.21757
19-Jul-06     Release date:   31-Jul-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06968  (DUT_ECOLI) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase
151 a.a.
137 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - dUTP diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: dUTP + H2O = dUMP + diphosphate
Bound ligand (Het Group name = DUD)
matches with 85.71% similarity
+ H(2)O
= dUMP
+ diphosphate
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   2 terms 
  Biological process     nucleotide metabolic process   5 terms 
  Biochemical function     hydrolase activity     4 terms  


DOI no: 10.1002/prot.21757 Proteins 71:308-319 (2008)
PubMed id: 17932923  
J.Kovári, O.Barabás, B.Varga, A.Békési, F.Tölgyesi, J.Fidy, J.Nagy, B.G.Vértessy.
  Selected figure(s)  
Figure 1.
Figure 1. (A) Reaction scheme of dUTP hydrolysis as catalyzed by dUTPases.[1] (B) The crystal structure of homotrimeric E. coli dUTPase: , -imino-dUTP:Mg complex (PDB ID: 1RN8). The three subunits of the enzyme are shown with ribbon model in green, blue, and yellow. The , -imino-dUTP ligands in the three identical active sites are in atom coloring bonds model (carbon, dark gray; oxygen, red; phosphorus, orange; nitrogen, blue; magnesium, purple).
Figure 2.
Figure 2. (A) Synthesis of 5 -O-tosyldeoxyuridine. (B) Synthesis of , -methylene-dUDP.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 308-319) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
20197546 Q.Ye, S.W.Crawley, Y.Yang, G.P.Côté, and Z.Jia (2010).
  Sci Signal, 3, ra17.
PDB codes: 3lkm 3lla 3lmh 3lmi
18837522 B.G.Vértessy, and J.Tóth (2009).
  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