Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.93 kDa 
• Atom Count: 2838 
• Modelled Residue Count: 329 
• Deposited Residue Count: 329 
• Unique protein chains: 1

2D2H

OpdA from Agrobacterium radiobacter with bound inhibitor trimethyl phosphate at 1.8 A resolution

• PDB DOI: 10.2210/pdb2D2H/pdb

• Classification: HYDROLASE
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-09-09 Released: 2005-09-20 
• Deposition Author(s): Jackson, C., Kim, H.K., Carr, P.D., Liu, J.W., Ollis, D.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism

Jackson, C., Kim, H.K., Carr, P.D., Liu, J.W., Ollis, D.L.

(2005) Biochim Biophys Acta 1752: 56-64

• PubMed: 16054447 
• DOI: 10.1016/j.bbapap.2005.06.008
• Primary Citation of Related Structures:  
  2D2G, 2D2H, 2D2J


• PubMed 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.

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Organizational Affiliation: 

Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphotriesterase	A	329	Agrobacterium tumefaciens	Mutation(s): 1  Gene Names: opdA EC: 3.1.8.1
UniProt
Find proteins for Q93LD7 (Rhizobium radiobacter) Explore Q93LD7  Go to UniProtKB:  Q93LD7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TZZ	D [auth A]	TRIMETHYL PHOSPHATE C3 H9 O4 P WVLBCYQITXONBZ-UHFFFAOYSA-N
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.926	α = 90
b = 108.926	β = 90
c = 62.345	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-09 
• Released Date: 2005-09-20 
Deposition Author(s): Jackson, C., Kim, H.K., Carr, P.D., Liu, J.W., Ollis, D.L.

Revision History  

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2015-08-19
  Changes: Non-polymer description