4RQZ

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

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

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

  • 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 ...

    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.


    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

    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA. Electronic address: bobsauer@mit.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protease degSA, B, C314Escherichia coliMutation(s): 0 
Gene Names: degSP12B_c3347
EC: 3.4.21.107
Find proteins for P0AEE3 (Escherichia coli (strain K12))
Explore P0AEE3 
Go to UniProtKB:  P0AEE3
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
activating peptideD, E, F10N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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 = 205.984α = 90
b = 142.71β = 89.24
c = 41.167γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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