3UBB

The crystal structure of GlpG in complex with a phosphonofluoridate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational Change in Rhomboid Protease GlpG Induced by Inhibitor Binding to Its S' Subsites.

Xue, Y.Chowdhury, S.Liu, X.Akiyama, Y.Ellman, J.Ha, Y.

(2012) Biochemistry 51: 3723-3731

  • DOI: 10.1021/bi300368b

  • PubMed Abstract: 
  • Rhomboid protease conducts proteolysis inside the hydrophobic environment of the membrane. The conformational flexibility of the protease is essential for the enzyme mechanism, but the nature of this flexibility is not completely understood. Here we ...

    Rhomboid protease conducts proteolysis inside the hydrophobic environment of the membrane. The conformational flexibility of the protease is essential for the enzyme mechanism, but the nature of this flexibility is not completely understood. Here we describe the crystal structure of rhomboid protease GlpG in complex with a phosphonofluoridate inhibitor, which is covalently bonded to the catalytic serine and extends into the S' side of the substrate binding cleft. Inhibitor binding causes subtle but extensive changes in the membrane protease. Many transmembrane helices tilt and shift positions, and the gap between S2 and S5 is slightly widened so that the inhibitor can bind between them. The side chain of Phe-245 from a loop (L5) that acts as a cap rotates and uncovers the opening of the substrate binding cleft to the lipid bilayer. A concurrent turn of the polypeptide backbone at Phe-245 moves the rest of the cap and exposes the catalytic serine to the aqueous solution. This study, together with earlier crystallographic investigation of smaller inhibitors, suggests a simple model for explaining substrate binding to rhomboid protease.


    Organizational Affiliation

    Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhomboid protease glpG
A
182Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: glpG
EC: 3.4.21.105
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Intramembrane Proteases
Protein: 
GlpG rhomboid-family intramembrane protease
Find proteins for P09391 (Escherichia coli (strain K12))
Go to UniProtKB:  P09391
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3UB
Query on 3UB

Download SDF File 
Download CCD File 
A
propan-2-yl hydrogen (S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}ethyl]phosphonate
C13 H20 N O5 P
DRLKMEFBZYZZJV-LLVKDONJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.211 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 111.722α = 90.00
b = 111.722β = 90.00
c = 121.810γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
CBASSdata collection
REFMACphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-10-24 
  • Released Date: 2012-06-13 
  • Deposition Author(s): Ha, Y., Xue, Y.

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description