Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.73 kDa 
• Atom Count: 6384 
• Modelled Residue Count: 873 
• Deposited Residue Count: 942 
• Unique protein chains: 1

1VCW

Crystal structure of DegS after backsoaking the activating peptide

• PDB DOI: 10.2210/pdb1VCW/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-16 Released: 2004-06-08 
• Deposition Author(s): Wilken, C., Kitzing, K., Kurzbauer, R., Ehrmann, M., Clausen, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.301 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4RR0

Literature

Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease.

Wilken, C., Kitzing, K., Kurzbauer, R., Ehrmann, M., Clausen, T.

(2004) Cell 117: 483-494

• PubMed: 15137941 
• DOI: 10.1016/s0092-8674(04)00454-4
• Primary Citation of Related Structures:  
  1SOT, 1SOZ, 1VCW


• PubMed Abstract: 
  

Gram-negative bacteria respond to misfolded proteins in the cell envelope with the sigmaE-driven expression of periplasmic proteases/chaperones. Activation of sigmaE is controlled by a proteolytic cascade that is initiated by the DegS protease. DegS senses misfolded protein in the periplasm, undergoes autoactivation, and cleaves the antisigma factor RseA. Here, we present the crystal structures of three distinct states of DegS from E. coli. DegS alone exists in a catalytically inactive form. Binding of stress-signaling peptides to its PDZ domain induces a series of conformational changes that activates protease function. Backsoaking of crystals containing the DegS-activator complex revealed the presence of an active/inactive hybrid structure and demonstrated the reversibility of activation. Taken together, the structural data illustrate in molecular detail how DegS acts as a periplasmic stress sensor. Our results suggest a novel regulatory role for PDZ domains and unveil a novel mechanism of reversible protease activation.

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Related Citations: 

• OMP peptide signals initiate the envelope-stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain
  Walsh, N.P., Alba, B.M., Bose, B., Gross, C.A., Sauer, R.T.
  (2003) Cell 113: 61

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Organizational Affiliation: 

Institute for Molecular Pathology (IMP), Dr. Bohrgasse 7, A-1030 Vienna, Austria.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease degS	A, B, C	314	Escherichia coli	Mutation(s): 0  Gene Names: degS, hhoB, htrH, b3235, Z4594, ECS4108 EC: 3.4.21 (PDB Primary Data), 3.4.21.107 (UniProt)
UniProt
Find proteins for P0AEE3 (Escherichia coli (strain K12)) Explore P0AEE3  Go to UniProtKB:  P0AEE3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 0.301 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 206.99	α = 90
b = 142.733	β = 90.09
c = 41.231	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-16 
• Released Date: 2004-06-08 
Deposition Author(s): Wilken, C., Kitzing, K., Kurzbauer, R., Ehrmann, M., Clausen, T.

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance