3B44

Crystal structure of GlpG W136A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG.

Wang, Y.Maegawa, S.Akiyama, Y.Ha, Y.

(2007) J.Mol.Biol. 374: 1104-1113

  • DOI: 10.1016/j.jmb.2007.10.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Intramembrane proteases are important enzymes in biology. The recently solved crystal structures of rhomboid protease GlpG have provided useful insights into the mechanism of these membrane proteins. Besides revealing an internal water-filled cavity ...

    Intramembrane proteases are important enzymes in biology. The recently solved crystal structures of rhomboid protease GlpG have provided useful insights into the mechanism of these membrane proteins. Besides revealing an internal water-filled cavity that harbored the Ser-His catalytic dyad, the crystal structure identified a novel structural domain (L1 loop) that lies on the side of the transmembrane helices. Here, using site-directed mutagenesis, we confirmed that the L1 loop is partially embedded in the membrane, and showed that alanine substitution of a highly preferred tryptophan (Trp136) at the distal tip of the L1 loop near the lipid:water interface reduced GlpG proteolytic activity. Crystallographic analysis showed that W136A mutation did not modify the structure of the protease. Instead, the polarity for a small and lipid-exposed protein surface at the site of the mutation has changed. The crystal structure, now refined at 1.7 A resolution, also clearly defined a 20-A-wide hydrophobic belt around the protease, which likely corresponded to the thickness of the compressed membrane bilayer around the protein. This improved structural model predicts that all critical elements of the catalysis, including the catalytic serine and the L5 cap, need to be positioned within a few angstroms of the membrane surface, and may explain why the protease activity is sensitive to changes in the protein:lipid interaction. Based on these findings, we propose a model where the end of the substrate transmembrane helix first partitions out of the hydrophobic core region of the membrane before it bends into the protease active site for cleavage.


    Organizational Affiliation

    Department of Pharmacology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glpG
A
180Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: glpG
EC: 3.4.21.105
Membrane protein
mpstruct
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
BNG
Query on BNG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 110.700α = 90.00
b = 110.700β = 90.00
c = 127.500γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance