2IAV

Crystal structure of squid ganglion DFPase H287A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1021/bi0500675
  • Primary Citation of Related Structures:  
    2IAV, 2IAW, 2IAX

  • 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. 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diisopropylfluorophosphatase312Loligo vulgarisMutation(s): 1 
EC: 3.1.8.2
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.07α = 90
b = 81.996β = 90
c = 86.627γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling

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: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description