4S3G

Structure of the F249X mutant of Phosphatidylinositol-specific phospholipase C from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fluorinated Aromatic Amino Acids Distinguish Cation-pi Interactions from Membrane Insertion.

He, T.Gershenson, A.Eyles, S.J.Lee, Y.J.Liu, W.R.Wang, J.Gao, J.Roberts, M.F.

(2015) J.Biol.Chem. 290: 19334-19342

  • DOI: 10.1074/jbc.M115.668343
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cation-π interactions, where protein aromatic residues supply π systems while a positive-charged portion of phospholipid head groups are the cations, have been suggested as important binding modes for peripheral membrane proteins. However, aromatic a ...

    Cation-π interactions, where protein aromatic residues supply π systems while a positive-charged portion of phospholipid head groups are the cations, have been suggested as important binding modes for peripheral membrane proteins. However, aromatic amino acids can also insert into membranes and hydrophobically interact with lipid tails. Heretofore there has been no facile way to differentiate these two types of interactions. We show that specific incorporation of fluorinated amino acids into proteins can experimentally distinguish cation-π interactions from membrane insertion of the aromatic side chains. Fluorinated aromatic amino acids destabilize the cation-π interactions by altering electrostatics of the aromatic ring, whereas their increased hydrophobicity enhances membrane insertion. Incorporation of pentafluorophenylalanine or difluorotyrosine into a Staphylococcus aureus phosphatidylinositol-specific phospholipase C variant engineered to contain a specific PC-binding site demonstrates the effectiveness of this methodology. Applying this methodology to the plethora of tyrosine residues in Bacillus thuringiensis phosphatidylinositol-specific phospholipase C definitively identifies those involved in cation-π interactions with phosphatidylcholine. This powerful method can easily be used to determine the roles of aromatic residues in other peripheral membrane proteins and in integral membrane proteins.


    Organizational Affiliation

    From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-phosphatidylinositol phosphodiesterase
A
302Staphylococcus aureus (strain Newman)Mutation(s): 0 
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
INS
Query on INS

Download SDF File 
Download CCD File 
A
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
MYO-INOSITOL
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PF5
Query on PF5
A
L-PEPTIDE LINKINGC9 H6 F5 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 60.050α = 90.00
b = 60.050β = 90.00
c = 191.330γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
CrystalCleardata collection
PHENIXrefinement
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Database references