4HDD

Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease.

Lazareno-Saez, C.Arutyunova, E.Coquelle, N.Lemieux, M.J.

(2013) J.Mol.Biol. 425: 1127-1142

  • DOI: 10.1016/j.jmb.2013.01.019

  • PubMed Abstract: 
  • Rhomboids are membrane-embedded serine proteases that cleave membrane protein substrates. Escherichia coli rhomboid GlpG (ecGlpG) consists of an N-terminal cytoplasmic domain and a membrane domain containing the active site. We determined the crystal ...

    Rhomboids are membrane-embedded serine proteases that cleave membrane protein substrates. Escherichia coli rhomboid GlpG (ecGlpG) consists of an N-terminal cytoplasmic domain and a membrane domain containing the active site. We determined the crystal structure of the soluble cytoplasmic domain of ecGlpG at 1.35Å resolution and examined whether this domain affected the catalytic activity of the enzyme. The structure revealed that the ecGlpG cytoplasmic domain exists as a dimer with extensive domain swapping between the two monomers. Domain-swapped dimers can be isolated from the full-length protein, suggesting that this is a physiologically relevant structure. An extensive steady-state kinetic analysis of the full-length ecGlpG and its membrane domain using soluble and transmembrane model protein substrates resulted in an unexpected conclusion: removal of the cytoplasmic domain does not alter the catalytic parameters for detergent-solubilized rhomboid for both substrates.


    Organizational Affiliation

    Membrane Protein Disease Research Group, Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhomboid protease GlpG
A
79Escherichia coli (strain K12)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
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 51.760α = 90.00
b = 51.760β = 90.00
c = 91.560γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
MxDCdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references