Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.54 kDa 
• Atom Count: 5344 
• Modelled Residue Count: 658 
• Deposited Residue Count: 662 
• Unique protein chains: 1

1EZ2

THREE-DIMENSIONAL STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE WITH BOUND SUBSTRATE ANALOG DIISOPROPYLMETHYL PHOSPHONATE.

• DOI: 10.2210/pdb1EZ2/pdb

• Classification: HYDROLASE
• Organism(s): Brevundimonas diminuta
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-05-09 Released: 2000-12-20 
• Deposition Author(s): Holden, H.M., Benning, M.M., Raushel, F.M., Hong, S.-B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.183 

Literature

The binding of substrate analogs to phosphotriesterase.

Benning, M.M., Hong, S.B., Raushel, F.M., Holden, H.M.

(2000) J Biol Chem 275: 30556-30560

• PubMed: 10871616 
• DOI: 10.1074/jbc.M003852200
• Primary Citation of Related Structures:  
  1EYW, 1EZ2


• PubMed Abstract: 
  

Phosphotriesterase (PTE) from Pseudomonas diminuta catalyzes the detoxification of organophosphates such as the widely utilized insecticide paraoxon and the chemical warfare agent sarin. The three-dimensional structure of the enzyme is known from high resolution x-ray crystallographic analyses. Each subunit of the homodimer folds into a so-called TIM barrel, with eight strands of parallel beta-sheet. The two zinc ions required for activity are positioned at the C-terminal portion of the beta-barrel. Here, we describe the three-dimensional structure of PTE complexed with the inhibitor diisopropyl methyl phosphonate, which serves as a mimic for sarin. Additionally, the structure of the enzyme complexed with triethyl phosphate is also presented. In the case of the PTE-diisopropyl methyl phosphonate complex, the phosphoryl oxygen of the inhibitor coordinates to the more solvent-exposed zinc ion (2.5 A), thereby lending support to the presumed catalytic mechanism involving metal coordination of the substrate. In the PTE-triethyl phosphate complex, the phosphoryl oxygen of the inhibitor is positioned at 3.4 A from the more solvent-exposed zinc ion. The two structures described in this report provide additional molecular understanding for the ability of this remarkable enzyme to hydrolyze such a wide range of organophosphorus substrates.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOTRIESTERASE	A, B	331	Brevundimonas diminuta	Mutation(s): 1  Gene Names: opd EC: 3.1.8.1
Find proteins for P0A434 (Brevundimonas diminuta) Explore P0A434  Go to UniProtKB:  P0A434

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DII	A, B	METHYLPHOSPHONIC ACID DIISOPROPYL ESTER C7 H17 O3 P WOAFDHWYKSOANX-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.183 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.4	α = 90
b = 91	β = 91.6
c = 69.2	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
FRAMBO	data collection
XDS	data scaling
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-09 
• Released Date: 2000-12-20 
Deposition Author(s): Holden, H.M., Benning, M.M., Raushel, F.M., Hong, S.-B.

Revision History  

• Version 1.0: 2000-12-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description