2IC8

Crystal structure of GlpG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a rhomboid family intramembrane protease.

Wang, Y.Zhang, Y.Ha, Y.

(2006) Nature 444: 179-180

  • DOI: 10.1038/nature05255

  • PubMed Abstract: 
  • Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and gamma-secretase, are unique in that they cleave the transmembrane domain of other membra ...

    Escherichia coli GlpG is an integral membrane protein that belongs to the widespread rhomboid protease family. Rhomboid proteases, like site-2 protease (S2P) and gamma-secretase, are unique in that they cleave the transmembrane domain of other membrane proteins. Here we describe the 2.1 A resolution crystal structure of the GlpG core domain. This structure contains six transmembrane segments. Residues previously shown to be involved in catalysis, including a Ser-His dyad, and several water molecules are found at the protein interior at a depth below the membrane surface. This putative active site is accessible by substrate through a large 'V-shaped' opening that faces laterally towards the lipid, but is blocked by a half-submerged loop structure. These observations indicate that, in intramembrane proteolysis, the scission of peptide bonds takes place within the hydrophobic environment of the membrane bilayer. The crystal structure also suggests a gating mechanism for GlpG that controls substrate access to its hydrophilic active site.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein glpG
A
182Escherichia coli (strain K12)Mutation(s): 0 
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: 2.1 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.236 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 110.822α = 90.00
b = 110.822β = 90.00
c = 127.611γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-09-12 
  • Released Date: 2006-10-17 
  • Deposition Author(s): Ha, Y.

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance