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PDBsum entry 1w2y

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1w2y
Jmol
Contents
Protein chains
226 a.a. *
209 a.a. *
Ligands
DUN ×2
Metals
_MG ×6
Waters ×383
* Residue conservation analysis
PDB id:
1w2y
Name: Hydrolase
Title: The crystal structure of a complex of campylobacter jejuni dutpase with substrate analogue dupnhp
Structure: Deoxyuridine 5'-triphosphate nucleotide hydrolase. Chain: a, b. Synonym: putative dutpase. Engineered: yes
Source: Campylobacter jejuni. Organism_taxid: 197. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.65Å     R-factor:   0.153     R-free:   0.194
Authors: O.V.Moroz,M.Harkiolaki,M.Y.Galperin,A.A.Vagin, D.Gonzalez-Pacanowska,K.S.Wilson
Key ref:
O.V.Moroz et al. (2004). The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases. J Mol Biol, 342, 1583-1597. PubMed id: 15364583 DOI: 10.1016/j.jmb.2004.07.050
Date:
09-Jul-04     Release date:   16-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q0P8G4  (Q0P8G4_CAMJE) -  DUTPase
Seq:
Struc:
229 a.a.
226 a.a.
Protein chain
Pfam   ArchSchema ?
Q0P8G4  (Q0P8G4_CAMJE) -  DUTPase
Seq:
Struc:
229 a.a.
209 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: 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 = DUN)
matches with 76.00% similarity
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.07.050 J Mol Biol 342:1583-1597 (2004)
PubMed id: 15364583  
 
 
The crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue sheds light on the mechanism and suggests the "basic module" for dimeric d(C/U)TPases.
O.V.Moroz, M.Harkiolaki, M.Y.Galperin, A.A.Vagin, D.González-Pacanowska, K.S.Wilson.
 
  ABSTRACT  
 
The crystal structure of the dUTPase from the important gastric pathogen Campylobacter jejuni has been solved at 1.65 A spacing. This essential bacterial enzyme is the second representative of the new family of dimeric dUTPases to be structurally characterised. Members of this family have a novel all-alpha fold and are unrelated to the all-beta dUTPases of the majority of organisms including eukaryotes such as humans, bacteria such as Escherichia coli, archaea like Methanococcus jannaschii and animal viruses. Therefore, dimeric dUTPases can be considered as candidate drug targets. The X-ray structure of the C.jejuni dUTPase in complex with the non-hydrolysable substrate analogue dUpNHp allows us to define the positions of three catalytically significant phosphate-binding magnesium ions and provides a starting point for a detailed understanding of the mechanism of dUTP/dUDP hydrolysis by dimeric dUTPases. Indeed, a water molecule present in the structure is ideally situated to act as the attacking nucleophile during hydrolysis. A comparison of the dUTPases from C.jejuni and Trypanosoma cruzi reveals a common fold with certain distinct features, both in the rigid and mobile domains as defined in the T.cruzi structure. Homologues of the C.jejuni dUTPase have been identified in several other bacteria and bacteriophages, including the dCTPase of phage T4. Sequence comparisons of these proteins define a new superfamily of d(C/U)TPases that includes three distinct enzyme families: (1) dUTPases in trypanosomatides, C.jejuni and several other Gram-negative bacteria, (2) predicted dUTPases in various Gram-positive bacteria and their phages, and (3) dCTP/dUTPases in enterobacterial T4-like phages. All these enzymes share a basic module that consists of two alpha-helices from the rigid domain, two helices from the mobile domain and connecting loops. These results in concert with a number of conserved residues responsible for interdomain cross-talk provide valuable insight towards rational drug design.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereoview of CjdUTPase dimer superimposed on the closed, ligand-bound form of the T. cruzi enzyme. CjdUTPase is shown in cyan and purple for the two subunits of the dimer and TcDUTPase is in red for both subunits. The structures were superimposed using the program LSQKAB.55
Figure 4.
Figure 4. (a) Stereo view of sugar-phosphate moiety of dUpNHp with bound magnesium ions. Two Mg ions coordinate the putative nucleophilic water. Conserved Mg-binding Asp and Glu residues are shown in blue, water molecules are shown in red. The nucleophilic water is indicated by an arrow, and the suggested direction of the nucleophilic attack is shown as a blue broken line. (b) Schematic representation of a hypothetical g-phosphate position. The g-phosphate was manually positioned into the crystal structure without any changes in protein residues and only required deletion of a single water molecule. In this rough model the distances between g-phosphate oxygen atoms and coordinating groups vary between 1.9 Å and 2.5 Å. It is possible that in the real situation two water molecules coordinated by Lys57 and Lys60 would be displaced by the g-phosphate group, which would allow the g-phosphate to have more appropriate coordination. The coordination by a Glu is unlikely and would at best require the side-chain to be protonated. The presence of a cluster of conserved lysine residues is a strong argument in favour of g-phosphate being positioned as described. With dUTP in a conformation close to that in the scheme there are no clashes with the proposed nucleophilic water W1. Blue arrow indicates the suggested direction of nucleophilic attack.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 1583-1597) copyright 2004.  
  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
19690365 E.J.Dodson, and M.M.Woolfson (2009).
ACORN2: new developments of the ACORN concept.
  Acta Crystallogr D Biol Crystallogr, 65, 881-891.  
19220460 M.Nonaka, D.Tsuchimoto, K.Sakumi, and Y.Nakabeppu (2009).
Mouse RS21-C6 is a mammalian 2'-deoxycytidine 5'-triphosphate pyrophosphohydrolase that prefers 5-iodocytosine.
  FEBS J, 276, 1654-1666.  
18560150 F.Javid-Majd, D.Yang, T.R.Ioerger, and J.C.Sacchettini (2008).
The 1.25 A resolution structure of phosphoribosyl-ATP pyrophosphohydrolase from Mycobacterium tuberculosis.
  Acta Crystallogr D Biol Crystallogr, 64, 627-635.
PDB codes: 1y6x 3c90
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
18094475 R.M.Keegan, and M.D.Winn (2008).
MrBUMP: an automated pipeline for molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 64, 119-124.  
18353782 S.Lee, M.H.Kim, B.S.Kang, J.S.Kim, G.H.Kim, Y.G.Kim, and K.J.Kim (2008).
Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response.
  J Biol Chem, 283, 15232-15240.
PDB codes: 3cra 3crc
17892463 A.Robinson, A.P.Guilfoyle, S.J.Harrop, Y.Boucher, H.W.Stokes, P.M.Curmi, and B.C.Mabbutt (2007).
A putative house-cleaning enzyme encoded within an integron array: 1.8 A crystal structure defines a new MazG subtype.
  Mol Microbiol, 66, 610-621.
PDB codes: 2q5z 2q73 2q9l
  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
16855307 J.X.Yao, E.J.Dodson, K.S.Wilson, and M.M.Woolfson (2006).
ACORN: a review.
  Acta Crystallogr D Biol Crystallogr, 62, 901-908.  
16359314 M.Y.Galperin, O.V.Moroz, K.S.Wilson, and A.G.Murzin (2006).
House cleaning, a part of good housekeeping.
  Mol Microbiol, 59, 5.  
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
16239723 Y.Jia-xing, M.M.Woolfson, K.S.Wilson, and E.J.Dodson (2005).
A modified ACORN to solve protein structures at resolutions of 1.7 A or better.
  Acta Crystallogr D Biol Crystallogr, 61, 1465-1475.  
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.