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.

Macromolecule Content

• Total Structure Weight: 103.41 kDa 
• Atom Count: 6253 
• Modelled Residue Count: 827 
• Deposited Residue Count: 972 
• Unique protein chains: 2

4RQZ

re-refinement of 1soz, Crystal Structure of DegS protease in complex with an activating peptide

• PDB DOI: 10.2210/pdb4RQZ/pdb

• Classification: Hydrolase/peptide
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-05 Released: 2015-03-11 
• Deposition Author(s): Sauer, R.T., Grant, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.226 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1soz

Literature

A Conserved Activation Cluster Is Required for Allosteric Communication in HtrA-Family Proteases.

de Regt, A.K., Kim, S., Sohn, J., Grant, R.A., Baker, T.A., Sauer, R.T.

(2015) Structure 23: 517-526

• PubMed: 25703375 
• DOI: 10.1016/j.str.2015.01.012
• Primary Citation of Related Structures:  
  4RQY, 4RQZ, 4RR0, 4RR1


• PubMed Abstract: 
  

In E. coli, outer-membrane stress causes a transcriptional response through a signaling cascade initiated by DegS cleavage of a transmembrane antisigma factor. Each subunit of DegS, an HtrA-family protease, contains a protease domain and a PDZ domain. The trimeric protease domain is autoinhibited by the unliganded PDZ domains. Allosteric activation requires binding of unassembled outer-membrane proteins (OMPs) to the PDZ domains and protein substrate binding. Here, we identify a set of DegS residues that cluster together at subunit-subunit interfaces in the trimer, link the active sites and substrate binding sites, and are crucial for stabilizing the active enzyme conformation in response to OMP signaling. These residues are conserved across the HtrA-protease family, including orthologs linked to human disease, supporting a common mechanism of allosteric activation. Indeed, mutation of residues at homologous positions in the DegP quality-control protease also eliminates allosteric activation.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA. Electronic address: [e-mail].

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, P12B_c3347 EC: 3.4.21.107
UniProt
Find proteins for P0AEE3 (Escherichia coli (strain K12)) Explore P0AEE3  Go to UniProtKB:  P0AEE3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
activating peptide	D, E, F	10	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.226 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 205.984	α = 90
b = 142.71	β = 89.24
c = 41.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-05 
• Released Date: 2015-03-11 
Deposition Author(s): Sauer, R.T., Grant, R.A.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references