4IYA

Structure of the Y250A mutant of the PANTON-VALENTINE LEUCOCIDIN S component from STAPHYLOCOCCUS AUREUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Residues essential for panton-valentine leukocidin s component binding to its cell receptor suggest both plasticity and adaptability in its interaction surface

Laventie, B.J.Guerin, F.Mourey, L.Tawk, M.Y.Jover, E.Maveyraud, L.Prevost, G.

(2014) Plos One 9: e92094-e92094

  • DOI: 10.1371/journal.pone.0092094
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Panton-Valentine leukocidin (PVL), a bicomponent staphylococcal leukotoxin, is involved in the poor prognosis of necrotizing pneumonia. The present study aimed to elucidate the binding mechanism of PVL and in particular its cell-binding domain. The c ...

    Panton-Valentine leukocidin (PVL), a bicomponent staphylococcal leukotoxin, is involved in the poor prognosis of necrotizing pneumonia. The present study aimed to elucidate the binding mechanism of PVL and in particular its cell-binding domain. The class S component of PVL, LukS-PV, is known to ensure cell targeting and exhibits the highest affinity for the neutrophil membrane (Kd∼10(-10) M) compared to the class F component of PVL, LukF-PV (Kd∼10(-9) M). Alanine scanning mutagenesis was used to identify the residues involved in LukS-PV binding to the neutrophil surface. Nineteen single alanine mutations were performed in the rim domain previously described as implicated in cell membrane interactions. Positions were chosen in order to replace polar or exposed charged residues and according to conservation between leukotoxin class S components. Characterization studies enabled to identify a cluster of residues essential for LukS-PV binding, localized on two loops of the rim domain. The mutations R73A, Y184A, T244A, H245A and Y250A led to dramatically reduced binding affinities for both human leukocytes and undifferentiated U937 cells expressing the C5a receptor. The three-dimensional structure of five of the mutants was determined using X-ray crystallography. Structure analysis identified residues Y184 and Y250 as crucial in providing structural flexibility in the receptor-binding domain of LukS-PV.


    Related Citations: 
    • Crystal structure of leucotoxin S component. New insight into the staphylococcal beta-barrel pore-forming toxins
      Guillet, V.,Roblin, P.,Werner, S.,Coraiola, M.,Menestrina, G.,Monteil, H.,Prevost, G.,Mourey, L.
      (2004) J.Biol.Chem. 279: 41028
    • The structure of a Staphylococcus aureus leucocidin component (LukF-PV) reveals the fold of the water-soluble species of a family of transmembrane pore-forming toxins
      Pedelacq, J.D.,Maveyraud, L.,Prevost, G.,Baba-moussa, L.,Gonzalez, A.,Courcelle, M.,Shepard, W.,Monteil, H.,Samama, J.P.,Mourey, L.
      (1999) Structure 7: 277
    • Crystallization and preliminary crystallographic data of leucotoxin S component from Staphylococcus aureus
      Guillet, V.,Keller, D.,Prevost, G.,Mourey, L.
      (2004) Acta Crystallogr.,Sect.D 60: 310


    Organizational Affiliation

    Université de Strasbourg-CHRU, Fédération de Médecine Translationnelle de Strasbourg, EA 7290 Virulence bactérienne précoce, Institut de Bactériologie, Strasbourg, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LukS-PV
A
292Staphylococcus phage PVLMutation(s): 1 
Find proteins for O80066 (Staphylococcus phage PVL)
Go to UniProtKB:  O80066
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.340α = 90.00
b = 89.320β = 90.00
c = 38.100γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2014-04-23
    Type: Database references