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PDBsum entry 1euw

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Hydrolase PDB id
1euw
Jmol
Contents
Protein chain
136 a.a. *
Ligands
EMC
GOL ×2
Waters ×286
* Residue conservation analysis
PDB id:
1euw
Name: Hydrolase
Title: Atomic resolution structure of e. Coli dutpase
Structure: Deoxyuridine 5'-triphosphate nucleotidohydrolase. Chain: a. Synonym: dutpase. Ec: 3.6.1.23
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Trimer (from PDB file)
Resolution:
1.05Å     R-factor:   0.141     R-free:   0.164
Authors: A.Gonzalez,E.Cedergren,G.Larsson,R.Persson
Key ref:
A.González et al. (2001). Atomic resolution structure of Escherichia coli dUTPase determined ab initio. Acta Crystallogr D Biol Crystallogr, 57, 767-774. PubMed id: 11375495 DOI: 10.1107/S0907444901004255
Date:
17-Apr-00     Release date:   03-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06968  (DUT_ECOLI) -  Deoxyuridine 5'-triphosphate nucleotidohydrolase
Seq:
Struc:
151 a.a.
136 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
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     nucleotide metabolic process   4 terms 
  Biochemical function     hydrolase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444901004255 Acta Crystallogr D Biol Crystallogr 57:767-774 (2001)
PubMed id: 11375495  
 
 
Atomic resolution structure of Escherichia coli dUTPase determined ab initio.
A.González, G.Larsson, R.Persson, E.Cedergren-Zeppezauer.
 
  ABSTRACT  
 
Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 A resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 A from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor-substrate-analogue complexes of this protein at very high resolution.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Detail of the 1.05 structure, showing parts of the polypeptide chain at the active site, including Tyr93 and one molecule of glycerol (Glyc139). The 2mF[o] - DF[c] electron-density map is contoured at 2 (in blue) and 4 (coral).
Figure 5.
Figure 5 View of the mercury-binding site in a 2mF[o] - DF[c] electron-density map contoured at 3 and 10 (in blue and orange, respectively) showing clearly the multiple conformations of the Hg atom (red spheres) bound to the S of Cys36.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 767-774) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460457 S.McNicholas, E.Potterton, K.S.Wilson, and M.E.Noble (2011).
Presenting your structures: the CCP4mg molecular-graphics software.
  Acta Crystallogr D Biol Crystallogr, 67, 386-394.  
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
16188990 A.J.Davison, and N.D.Stow (2005).
New genes from old: redeployment of dUTPase by herpesviruses.
  J Virol, 79, 12880-12892.  
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
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 codes are shown on the right.