3ZEB

A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Activity-Based Probes for Rhomboid Proteases Discovered in a Mass Spectrometry-Based Assay.

Vosyka, O.Vinothkumar, K.R.Wolf, E.V.Brouwer, A.J.Liskamp, R.M.J.Verhelst, S.H.L.

(2013) Proc.Natl.Acad.Sci.USA 110: 2472

  • DOI: 10.1073/pnas.1215076110

  • PubMed Abstract: 
  • Rhomboid proteases are evolutionary conserved intramembrane serine proteases. Because of their emerging role in many important biological pathways, rhomboids are potential drug targets. Unfortunately, few chemical tools are available for their study. ...

    Rhomboid proteases are evolutionary conserved intramembrane serine proteases. Because of their emerging role in many important biological pathways, rhomboids are potential drug targets. Unfortunately, few chemical tools are available for their study. Here, we describe a mass spectrometry-based assay to measure rhomboid substrate cleavage and inhibition. We have identified isocoumarin inhibitors and developed activity-based probes for rhomboid proteases. The probes can distinguish between active and inactive rhomboids due to covalent, reversible binding of the active-site serine and stable modification of a histidine residue. Finally, the structure of an isocoumarin-based inhibitor with Escherichia coli rhomboid GlpG uncovers an unusual mode of binding at the active site and suggests that the interactions between the 3-substituent on the isocoumarin inhibitor and hydrophobic residues on the protease reflect S' subsite binding. Overall, these probes represent valuable tools for rhomboid study, and the structural insights may facilitate future inhibitor design.


    Organizational Affiliation

    Center for Integrated Protein Science Munich, Lehrstuhl für Chemie der Biopolymere, Technische Universität München, 85354 Freising, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHOMBOID PROTEASE GLPG
A
179Escherichia coli (strain K12)Gene Names: glpG
EC: 3.4.21.105
Find proteins for P09391 (Escherichia coli (strain K12))
Go to UniProtKB:  P09391
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SV1
Query on SV1

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Download CCD File 
A
2-phenylethyl 2-(4-azanyl-2-methanoyl-phenyl)ethanoate
C17 H17 N O3
VKURJRUODVXQJZ-UHFFFAOYSA-N
 Ligand Interaction
BNG
Query on BNG

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Download CCD File 
A
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 111.109α = 90.00
b = 111.109β = 90.00
c = 126.067γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references