2QF3

Structure of the delta PDZ truncation of the DegS protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Allosteric activation of DegS, a stress sensor PDZ protease.

Sohn, J.Grant, R.A.Sauer, R.T.

(2007) Cell 131: 572-583

  • DOI: 10.1016/j.cell.2007.08.044
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Regulated intramembrane proteolysis is a method for transducing signals between cellular compartments. When protein folding is compromised in the periplasm of E. coli, the C termini of outer-membrane proteins (OMPs) bind to the PDZ domains of the tri ...

    Regulated intramembrane proteolysis is a method for transducing signals between cellular compartments. When protein folding is compromised in the periplasm of E. coli, the C termini of outer-membrane proteins (OMPs) bind to the PDZ domains of the trimeric DegS protease and activate cleavage of RseA, a transmembrane transcriptional regulator. We show here that DegS is an allosteric enzyme. OMP binding shifts the equilibrium from a nonfunctional state, in which the active sites are unreactive, to the functional proteolytic conformation. Crystallographic, biochemical, and mutagenic experiments show that the unliganded PDZ domains are inhibitory and suggest that OMP binding per se is sufficient to stabilize the relaxed conformation and activate DegS. OMP-induced activation and RseA binding are both positively cooperative, allowing switch-like behavior of the OMP-DegS-RseA system. Residues involved in the DegS allosteric switch are conserved in the DegP/HtrA and HtrA2/Omi families, suggesting that many PDZ proteases use a common mechanism of allosteric activation.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease degS
A, B, C
243Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: degS (hhoB, htrH)
EC: 3.4.21.107
Find proteins for P0AEE3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEE3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.347α = 90.00
b = 75.316β = 90.00
c = 162.257γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
AMoREphasing
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description