3V16

An intramolecular pi-cation latch in phosphatidylinositol-specific phospholipase C from S.aureus controls substrate access to the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the S. aureus PI-Specific Phospholipase C Reveals Modulation of Active Site Access by a Titratable PI-Cation Latched Loop

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

(2012) Biochemistry 51: 2579-2587

  • DOI: 10.1021/bi300057q
  • Primary Citation of Related Structures:  
    3V1H, 3V16, 3V18

  • PubMed Abstract: 
  • Staphylococcus aureus secretes a phosphatidylinositol-specific phospholipase C (PI-PLC) as a virulence factor that is unusual in exhibiting higher activity at acidic pH values than other enzymes in this class. We have determined the crystal structure ...

    Staphylococcus aureus secretes a phosphatidylinositol-specific phospholipase C (PI-PLC) as a virulence factor that is unusual in exhibiting higher activity at acidic pH values than other enzymes in this class. We have determined the crystal structure of this enzyme at pH 4.6 and pH 7.5. Under slightly basic conditions, the S. aureus PI-PLC structure closely follows the conformation of other bacterial PI-PLCs. However, when crystallized under acidic conditions, a large section of mobile loop at the αβ-barrel rim in the vicinity of the active site shows ~10 Å shift. This loop displacement at acidic pH is the result of a titratable intramolecular π-cation interaction between His258 and Phe249. This was verified by a structure of the mutant protein H258Y crystallized at pH 4.6, which does not exhibit the large loop shift. The intramolecular π-cation interaction for S. aureus PI-PLC provides an explanation for the activity of the enzyme at acid pH and also suggests how phosphatidylcholine, as a competitor for Phe249, may kinetically activate this enzyme.


    Organizational Affiliation

    Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1-phosphatidylinositol phosphodiesteraseA303Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 0 
Gene Names: plcNWMN_0041
EC: 4.6.1.13
Find proteins for P45723 (Staphylococcus aureus (strain Newman))
Explore P45723 
Go to UniProtKB:  P45723
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INS
Query on INS

Download Ideal Coordinates CCD File 
A
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.161α = 90
b = 43.607β = 90
c = 62.218γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CrystalCleardata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Other
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description