2HUC

Structural Studies Examining the Substrate Specificity Profiles of PC-PLCBc Protein Variants


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.208 

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This is version 1.5 of the entry. See complete history


Literature

Structural studies examining the substrate specificity profiles of PC-PLC(Bc) protein variants.

Benfield, A.P.Goodey, N.M.Phillips, L.T.Martin, S.F.

(2007) Arch Biochem Biophys 460: 41-47

  • DOI: https://doi.org/10.1016/j.abb.2007.01.023
  • Primary Citation of Related Structures:  
    2FFZ, 2FGN, 2HUC

  • PubMed Abstract: 

    The phosphatidylcholine preferring phospholipase C from Bacillus cereus (PC-PLC(Bc)) catalyzes the hydrolysis of phospholipids in the following order of preference: phosphatidylcholine (PC)>phosphatidylethanolamine (PE)>phosphatidylserine (PS). In previous work, mutagenic, kinetic, and crystallographic experiments suggested that varying the amino acids at the 4th, 56th, and 66th positions had a significant influence upon the substrate specificity profile of PC-PLC(Bc). Here, we report the crystal structures of the native form of several PC-PLC(Bc) variants that exhibited altered substrate specificities for PC, PE, and PS at maximum resolutions of 1.90-2.05 Angstrom. Comparing the structures of these variants to the structure of the wild-type enzyme reveals only minor differences with respect to the number and location of active site water molecules and the side chain conformations of residues at the 4th and 56th positions. These results suggest that subtle changes in steric and electronic properties in the substrate binding site of PC-PLC(Bc) are responsible for the significant changes in substrate selectivity.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, The University of Texas, 1 University Station - A5300, Austin, TX 78712, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipase C245Bacillus cereusMutation(s): 1 
Gene Names: plc
EC: 3.1.4.3
UniProt
Find proteins for P09598 (Bacillus cereus)
Explore P09598 
Go to UniProtKB:  P09598
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09598
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.973α = 90
b = 89.973β = 90
c = 71.957γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    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: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection