2IC8

Crystal structure of GlpG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.236 

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This is version 1.3 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
  • Primary Citation of Related Structures:  
    2IC8

  • 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 membrane proteins ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein glpGA182Escherichia coliMutation(s): 0 
Gene Names: glpGb3424
EC: 3.4.21.105
Membrane Entity: Yes 
UniProt
Find proteins for P09391 (Escherichia coli (strain K12))
Explore P09391 
Go to UniProtKB:  P09391
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 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
b = 110.822β = 90
c = 127.611γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary