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PDBsum entry 2d2h
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protein ligands metals links
Hydrolase PDB id
2d2h

 

 

 

 

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Contents
Protein chain
329 a.a. *
Ligands
TZZ
Metals
_CO ×2
Waters ×317
* Residue conservation analysis
PDB id:
2d2h
Name: Hydrolase
Title: Opda from agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 a resolution
Structure: Phosphotriesterase. Chain: a. Fragment: residues 33-361. Synonym: opda. Engineered: yes. Mutation: yes
Source: Agrobacterium tumefaciens. Organism_taxid: 358. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.189     R-free:   0.214
Authors: C.Jackson,H.K.Kim,P.D.Carr,J.W.Liu,D.L.Ollis
Key ref: C.Jackson et al. (2005). The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism. Biochim Biophys Acta, 1752, 56-64. PubMed id: 16054447
Date:
09-Sep-05     Release date:   20-Sep-05    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q93LD7  (Q93LD7_RHIRD) -  Phosphotriesterase from Rhizobium radiobacter
Seq:
Struc: 		384 a.a.
329 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.8.1  - aryldialkylphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol
aryl dialkyl phosphate
 + H2O
 =
dialkyl phosphate
Bound ligand (Het Group name = TZZ)
matches with 50.00% similarity 		+ aryl alcohol
      Cofactor: Divalent cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
Biochim Biophys Acta 1752:56-64 (2005)
PubMed id: 16054447  
 
 
The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism.
C.Jackson, H.K.Kim, P.D.Carr, J.W.Liu, D.L.Ollis.
 
  ABSTRACT  
 
A detailed understanding of the catalytic mechanism of enzymes is an important step toward improving their activity for use in biotechnology. In this paper, crystal soaking experiments and X-ray crystallography were used to analyse the mechanism of the Agrobacterium radiobacter phosphotriesterase, OpdA, an enzyme capable of detoxifying a broad range of organophosphate pesticides. The structures of OpdA complexed with ethylene glycol and the product of dimethoate hydrolysis, dimethyl thiophosphate, provide new details of the catalytic mechanism. These structures suggest that the attacking nucleophile is a terminally bound hydroxide, consistent with the catalytic mechanism of other binuclear metallophosphoesterases. In addition, a crystal structure with the potential substrate trimethyl phosphate bound non-productively demonstrates the importance of the active site cavity in orienting the substrate into an approximation of the transition state.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21190057 J.S.Fraser, and C.J.Jackson (2011).
Mining electron density for functionally relevant protein polysterism in crystal structures.
  Cell Mol Life Sci, 68, 1829-1841.  
19691327 J.A.Larrabee, W.R.Johnson, and A.S.Volwiler (2009).
Magnetic circular dichroism study of a dicobalt(II) complex with mixed 5- and 6-coordination: a spectroscopic model for dicobalt(II) hydrolases.
  Inorg Chem, 48, 8822-8829.  
19247785 P.Del Vecchio, M.Elias, L.Merone, G.Graziano, J.Dupuy, L.Mandrich, P.Carullo, B.Fournier, D.Rochu, M.Rossi, P.Masson, E.Chabriere, and G.Manco (2009).
Structural determinants of the high thermal stability of SsoPox from the hyperthermophilic archaeon Sulfolobus solfataricus.
  Extremophiles, 13, 461-470.  
19353598 X.Zhang, R.Wu, L.Song, Y.Lin, M.Lin, Z.Cao, W.Wu, and Y.Mo (2009).
Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase.
  J Comput Chem, 30, 2388-2401.  
  18678932 C.J.Jackson, K.S.Hadler, P.D.Carr, A.J.Oakley, S.Yip, G.Schenk, and D.L.Ollis (2008).
Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 681-685.
PDB codes: 2zo9 2zoa
18702530 J.Kim, P.C.Tsai, S.L.Chen, F.Himo, S.C.Almo, and F.M.Raushel (2008).
Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.
  Biochemistry, 47, 9497-9504.
PDB codes: 2o4q 3cak 3cs2
18535849 R.E.Mirams, S.J.Smith, K.S.Hadler, D.L.Ollis, G.Schenk, and L.R.Gahan (2008).
Cadmium(II) complexes of the glycerophosphodiester-degrading enzyme GpdQ and a biomimetic N,O ligand.
  J Biol Inorg Chem, 13, 1065-1072.  
16699182 D.E.Danley (2006).
Crystallization to obtain protein-ligand complexes for structure-aided drug design.
  Acta Crystallogr D Biol Crystallogr, 62, 569-575.  
16327895 C.J.Jackson, J.W.Liu, M.L.Coote, and D.L.Ollis (2005).
The effects of substrate orientation on the mechanism of a phosphotriesterase.
  Org Biomol Chem, 3, 4343-4350.  
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.

 

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