X-ray Structure of the R70D PI-PLC enzyme: Insight into the role of calcium and surrounding amino acids on active site geometry and catalysis.

Experimental Data Snapshot

  • Resolution: 2.11 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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X-ray Structure of the R69D Phosphatidylinositol-Specific Phospholipase C Enzyme: Insight into the Role of Calcium and Surrounding Amino Acids in Active Site Geometry and Catalysis.

Apiyo, D.Zhao, L.Tsai, M.-D.Selby, T.L.

(2005) Biochemistry 44: 9980-9989

  • DOI: https://doi.org/10.1021/bi047896v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Phosphatidylinositol-specific phospholipase Cs (PLCs) are a family of phosphodiesterases that catalyze the cleavage of the P-O bond via transesterification using the internal hydroxyl group of the substrate as a nucleophile, generating the five-membered cyclic inositol phosphate as an intermediate or product. To better understand the role of calcium in the catalytic mechanism of PLCs, we have determined the X-ray crystal structure of an engineered PLC enzyme from Bacillus thuringiensis to 2.1 A resolution. The active site of this enzyme has been altered by substituting the catalytic arginine with an aspartate at position 69 (R69D). This single-amino acid substitution converted a metal-independent, low-molecular weight enzyme into a metal ion-dependent bacterial PLC with an active site architecture similar to that of the larger metal ion-dependent mammalian PLC. The Ca(2+) ion shows a distorted square planar geometry in the active site that allows for efficient substrate binding and transition state stabilization during catalysis. Additional changes in the positions of the catalytic general acid/general base (GA/GB) were also observed, indicating the interrelation of the intricate hydrogen bonding network involved in stabilizing the active site amino acids. The functional information provided by this X-ray structure now allows for a better understanding of the catalytic mechanism, including stereochemical effects and substrate interactions, which facilitates better inhibitor design and sheds light on the possibilities of understanding how protein evolution might have occurred across this enzyme family.

  • Organizational Affiliation

    Department of Chemistry, The University of Central Florida, Orlando, Florida 32816, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-phosphatidylinositol phosphodiesterase
A, B
299Bacillus thuringiensisMutation(s): 1 
Membrane Entity: Yes 
Find proteins for P08954 (Bacillus thuringiensis)
Explore P08954 
Go to UniProtKB:  P08954
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08954
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.11 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.221α = 90
b = 147.725β = 90
c = 96.562γ = 90
Software Package:
Software NamePurpose
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: 2005-08-16
    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: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection