3M9G

Crystal structure of the three-PASTA-domain of a Ser/Thr kinase from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Extended Conformation of the 2.9-A Crystal Structure of the Three-PASTA Domain of a Ser/Thr Kinase from the Human Pathogen Staphylococcus aureus

Paracuellos, P.Ballandras, A.Robert, X.Kahn, R.Herve, M.Mengin-Lecreulx, D.Cozzone, A.J.Duclos, B.Gouet, P.

(2010) J.Mol.Biol. 404: 847-858

  • DOI: 10.1016/j.jmb.2010.10.012

  • PubMed Abstract: 
  • PASTA (penicillin-binding protein and serine/threonine kinase associated) modules are found in penicillin-binding proteins and bacterial serine/threonine kinases mainly from Gram-positive Firmicutes and Actinobacteria. They may act as extracellular s ...

    PASTA (penicillin-binding protein and serine/threonine kinase associated) modules are found in penicillin-binding proteins and bacterial serine/threonine kinases mainly from Gram-positive Firmicutes and Actinobacteria. They may act as extracellular sensors by binding peptidoglycan fragments. We report here the first crystal structure of a multiple-PASTA domain from Ser/Thr kinase, that of the protein serine/threonine kinase 1 (Stk1) from the Firmicute Staphylococcus aureus. The extended conformation of the three PASTA subunits differs strongly from the compact conformation observed in the two-PASTA domain of penicillin-binding protein PBP2x, whereas linear conformations were also reported for two-subunit fragments of the four-PASTA domain of the Actinobacteria Mycobacterium tuberculosis studied by liquid NMR. Thus, a stretched organization appears to be the signature of modular PASTA domains in Ser/Thr kinases. Signal transduction to the kinase domain is supposed to occur via dimerization and ligand binding. A conserved X-shaped crystallographic dimer stabilized by intermolecular interactions between the second PASTA subunits of each monomer is observed in the two crystal forms of Stk1 that we managed to crystallize. Extracellular PASTA domains are composed of at least two subunits, and this molecular assembly is a plausible candidate for the biological dimer. We have also performed docking experiments, which predict that the hinge regions of the PASTA domain can accommodate peptidoglycan. Finally, a three-dimensional homology molecular model of full-length Stk1 was generated, suggesting an interaction between the kinase domain and the cytoplasmic face of the plasma membrane via a eukaryotic-like juxtamembrane domain. A comprehensive activation mechanism for bacterial Ser/Thr kinases is proposed with the support of these structural data.


    Related Citations: 
    • Crystallization and initial X-ray diffraction study of the three PASTA domains of the Ser/Thr kinase Stk1 from the human pathogen Staphylococcus aureus
      Paracuellos, P.,Ballandras, A.,Robert, X.,Cozzone, A.J.,Duclos, B.,Gouet, P.
      (2009) Acta Crystallogr.,Sect.F 65: 1187


    Organizational Affiliation

    Laboratoire de Phosphorylation des Protéines et Pathogénie Bactérienne, Institut de Biologie et Chimie des Protéines, UMR 5086-CNRS/Université de Lyon, IFR128 BioSciences Gerland Lyon Sud, 7 Passage du Vercors, F-69367 Lyon cedex 07, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein kinase
A
201Staphylococcus aureus (strain N315)Mutation(s): 0 
Find proteins for A0A0H3JME9 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  A0A0H3JME9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 91.860α = 90.00
b = 101.210β = 90.00
c = 74.750γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
REFMACrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance