3V18

Structure of the Phosphatidylinositol-specific phospholipase C from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  3V16, 3V1H

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-phosphatidylinositol phosphodiesterase
A
304Staphylococcus aureus (strain Newman)Gene Names: plc
EC: 4.6.1.13
Find proteins for P45723 (Staphylococcus aureus (strain Newman))
Go to UniProtKB:  P45723
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IPA
Query on IPA

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Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.352α = 90.00
b = 58.001β = 90.00
c = 61.725γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
CNSrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Other