4F2B

Modulation of S.Aureus Phosphatidylinositol-Specific Phospholipase C Membrane Binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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This is version 1.1 of the entry. See complete history


Literature

Competition between Anion Binding and Dimerization Modulates Staphylococcus aureus Phosphatidylinositol-specific Phospholipase C Enzymatic Activity.

Cheng, J.Goldstein, R.Stec, B.Gershenson, A.Roberts, M.F.

(2012) J Biol Chem 287: 40317-40327

  • DOI: https://doi.org/10.1074/jbc.M112.395277
  • Primary Citation of Related Structures:  
    4F2B, 4F2T, 4F2U

  • PubMed Abstract: 

    Bacterial phosphatidylinositol-specific phospholipase C targets PI and glycosylphosphatidylinositol-linked proteins of eukaryotic cells. Functional relevance of a homodimeric S. aureus PI-PLC crystal structure is supported by enzyme kinetics and mutagenesis. Nonsubstrate phosphatidylcholine increases activity by facilitating enzyme dimerization. Activating transient dimerization is antagonized by anions binding to a discrete site. Interplay of protein oligomerization and anion binding controls enzyme activity. Staphylococcus aureus phosphatidylinositol-specific phospholipase C (PI-PLC) is a secreted virulence factor for this pathogenic bacterium. A novel crystal structure shows that this PI-PLC can form a dimer via helix B, a structural feature present in all secreted, bacterial PI-PLCs that is important for membrane binding. Despite the small size of this interface, it is critical for optimal enzyme activity. Kinetic evidence, increased enzyme specific activity with increasing enzyme concentration, supports a mechanism where the PI-PLC dimerization is enhanced in membranes containing phosphatidylcholine (PC). Mutagenesis of key residues confirm that the zwitterionic phospholipid acts not by specific binding to the protein, but rather by reducing anionic lipid interactions with a cationic pocket on the surface of the S. aureus enzyme that stabilizes monomeric protein. Despite its structural and sequence similarity to PI-PLCs from other Gram-positive pathogenic bacteria, S. aureus PI-PLC appears to have a unique mechanism where enzyme activity is modulated by competition between binding of soluble anions or anionic lipids to the cationic sensor and transient dimerization on the membrane.


  • Organizational Affiliation

    Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-phosphatidylinositol phosphodiesterase
A, B
310Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 0 
Gene Names: plcNWMN_0041
EC: 4.6.1.13
UniProt
Find proteins for P45723 (Staphylococcus aureus (strain Newman))
Explore P45723 
Go to UniProtKB:  P45723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45723
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
INS
Query on INS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.362α = 90
b = 133.382β = 89.95
c = 50.19γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description