2IAX

Crystal structure of squid ganglion DFPase D232S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mutational and structural studies of the diisopropylfluorophosphatase from Loligo vulgaris shed new light on the catalytic mechanism of the enzyme

Katsemi, V.Luecke, C.Koepke, J.Loehr, F.Maurer, S.Fritzsch, G.Rueterjans, H.

(2005) Biochemistry 44: 9022-9033

  • DOI: 10.1021/bi0500675
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The active site, the substrate binding site, and the metal binding sites of the diisopropylfluorophosphatase (DFPase) from Loligo vulgaris have been modified by means of site-directed mutagenesis to improve our understanding of the reaction mechanism ...

    The active site, the substrate binding site, and the metal binding sites of the diisopropylfluorophosphatase (DFPase) from Loligo vulgaris have been modified by means of site-directed mutagenesis to improve our understanding of the reaction mechanism. Enzymatic characterization of mutants located in the major groove of the substrate binding pocket indicates that large hydrophobic side chains at these positions are favorable for substrate turnover. Moreover, the active site residue His287 proved to be beneficial, but not essential, for DFP hydrolysis. In most cases, hydrophobic side chains at position 287 led to significant catalytic activities although reduced relative to the wild-type enzyme. With respect to the Ca-1 binding site, where catalysis occurs, various mutants indicated that the net charge at this calcium-binding site as well as the relative positions of the charged calcium ligands is crucial for catalytic activity. The importance of the electrostatic potential at the active site was furthermore revealed by various mutations of residues lining the interior of the central water-filled tunnel, which traverses the entire protein structure. In this respect, the structural features of residue His181, which is located at the opposite end of the DFPase tunnel relative to the active site, were characterized extensively. It was concluded that a tunnel-spanning hydrogen bond network, which includes a large number of apparently slow exchanging water molecules, relays any modifications in the electrostatics of the system to the active site, thus affecting the catalytic reactivity of the enzyme.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of DFPase from Loligo vulgaris
      Scharff, E.I.,Luecke, C.,Fritzsch, G.,Koepke, J.,Hartleib, J.,Dierl, S.,Rueterjans, H.
      (2001) Acta Crystallogr.,Sect.D 57: 148
    • Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris
      Scharff, E.I.,Koepke, J.,Fritzsch, G.,Luecke, C.,Rueterjans, H.
      (2001) Structure 9: 493
    • Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution
      Koepke, J.,Scharff, E.I.,Luecke, C.,Rueterjans, H.,Fritzsch, G.
      (2003) Acta Crystallogr.,Sect.D 59: 1744


    Organizational Affiliation

    Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, J. W. Goethe University of Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diisopropylfluorophosphatase
A
312Loligo vulgarisMutation(s): 1 
EC: 3.1.8.2
Find proteins for Q7SIG4 (Loligo vulgaris)
Go to UniProtKB:  Q7SIG4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.081α = 90.00
b = 82.053β = 90.00
c = 86.631γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALEPACKdata scaling
MAR345data collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description