2IAO

Crystal structure of squid ganglion DFPase E37Q mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris

Scharff, E.I.Koepke, J.Fritzsch, G.Luecke, C.Rueterjans, H.

(2001) Structure 9: 493-502

  • DOI: https://doi.org/10.1016/s0969-2126(01)00610-4
  • Primary Citation of Related Structures:  
    1E1A, 2IAO, 2IAP, 2IAQ, 2IAR, 2IAS, 2IAT, 2IAU

  • PubMed Abstract: 

    Phosphotriesterases (PTE) are enzymes capable of detoxifying organophosphate-based chemical warfare agents by hydrolysis. One subclass of these enzymes comprises the family of diisopropylfluorophosphatases (DFPases). The DFPase reported here was originally isolated from squid head ganglion of Loligo vulgaris and can be characterized as squid-type DFPase. It is capable of hydrolyzing the organophosphates diisopropylfluorophosphate, soman, sarin, tabun, and cyclosarin. Crystals were grown of both the native and the selenomethionine-labeled enzyme. The X-ray crystal structure of the DFPase from Loligo vulgaris has been solved by MAD phasing and refined to a crystallographic R value of 17.6% at a final resolution of 1.8 A. Using site-directed mutagenesis, we have structurally and functionally characterized essential residues in the active site of the enzyme. The crystal structure of the DFPase from Loligo vulgaris is the first example of a structural characterization of a squid-type DFPase and the second crystal structure of a PTE determined to date. Therefore, it may serve as a structural model for squid-type DFPases in general. The overall structure of this protein represents a six-fold beta propeller with two calcium ions bound in a central water-filled tunnel. The consensus motif found in the blades of this beta propeller has not yet been observed in other beta propeller structures. Based on the results obtained from mutants of active-site residues, a mechanistic model for the DFP hydrolysis has been developed.


  • Organizational Affiliation

    Institute of Biophysical Chemistry, Johann Wolfgang Goethe-University, Marie-Curie-Strasse 9, D-60439, Frankfurt/Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIISOPROPYLFLUOROPHOSPHATASE312Loligo vulgarisMutation(s): 1 
EC: 3.1.8.2 (PDB Primary Data), 3.8.2.2 (UniProt)
UniProt
Find proteins for Q7SIG4 (Loligo vulgaris)
Explore Q7SIG4 
Go to UniProtKB:  Q7SIG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIG4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.901α = 90
b = 81.696β = 90
c = 86.246γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description