6EW9

CRYSTAL STRUCTURE OF DEGS STRESS SENSOR PROTEASE IN COMPLEX WITH ACTIVATING DNRLGLVYQF PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of Noncatalytic Lysine Residues from Allosteric Circuits via Covalent Probes.

Bongard, J.Lorenz, M.Vetter, I.R.Stege, P.Porfetye, A.T.Schmitz, A.L.Kaschani, F.Wolf, A.Koch, U.Nussbaumer, P.Klebl, B.Kaiser, M.Ehrmann, M.

(2018) ACS Chem Biol 13: 1307-1312

  • DOI: 10.1021/acschembio.8b00101
  • Primary Citation of Related Structures:  
    6EW9

  • PubMed Abstract: 
  • Covalent modifications of nonactive site lysine residues by small molecule probes has recently evolved into an important strategy for interrogating biological systems. Here, we report the discovery of a class of bioreactive compounds that covalently modify lysine residues in DegS, the rate limiting protease of the essential bacterial outer membrane stress response pathway ...

    Covalent modifications of nonactive site lysine residues by small molecule probes has recently evolved into an important strategy for interrogating biological systems. Here, we report the discovery of a class of bioreactive compounds that covalently modify lysine residues in DegS, the rate limiting protease of the essential bacterial outer membrane stress response pathway. These modifications lead to an allosteric activation and allow the identification of novel residues involved in the allosteric activation circuit. These findings were validated by structural analyses via X-ray crystallography and cell-based reporter systems. We anticipate that our findings are not only relevant for a deeper understanding of the structural basis of allosteric activation in DegS and other HtrA serine proteases but also pinpoint an alternative use of covalent small molecules for probing essential biochemical mechanisms.


    Organizational Affiliation

    Microbiology, Faculty of Biology, Zentrum für Medizinische Biotechnologie (ZMB) , Universität Duisburg-Essen , Universitätsstr. 2 , 45117 Essen , Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine endoprotease DegSA, B, C315Escherichia coli K-12Mutation(s): 0 
Gene Names: degShhoBhtrHb3235JW3204
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
DNRLGLVYQF PEPTIDED [auth P], E [auth Q], F [auth R]10synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.6α = 90
b = 53.65β = 101.8
c = 132.5γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCRC1093

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-07
    Changes: Data collection, Source and taxonomy