6PJR

Time-resolved structural snapshot of proteolysis by GlpG inside the membrane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release.

Cho, S.Baker, R.P.Ji, M.Urban, S.

(2019) Nat Struct Mol Biol 26: 910-918

  • DOI: 10.1038/s41594-019-0296-9
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein cleavage inside the cell membrane triggers various pathophysiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing ...

    Protein cleavage inside the cell membrane triggers various pathophysiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing time-resolved steps that encompass the entire proteolytic reaction on a transmembrane substrate and an aldehyde inhibitor. Extensive gate opening accompanied substrate, but not inhibitor, binding, revealing that substrates and inhibitors take different paths to the active site. Catalysis unexpectedly commenced with, and was guided through subsequent catalytic steps by, motions of an extracellular loop, with local contributions from active site residues. We even captured the elusive tetrahedral intermediate that is uncleaved but covalently attached to the catalytic serine, about which the substrate was forced to bend dramatically. This unexpectedly stable intermediate indicates rhomboid catalysis uses an unprecedented reaction coordinate that may involve mechanically stressing the peptide bond, and could be selectively targeted by inhibitors.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA. rhomboidprotease@gmail.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhomboid protease GlpG
A
211Escherichia coliMutation(s): 1 
Gene Names: 
EC: 3.4.21.105
Find proteins for A0A0J2E248 (Escherichia coli)
Go to UniProtKB:  A0A0J2E248
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide aldehyde inhibitor
B
13Drosophila melanogasterMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.28α = 90
b = 99.88β = 90
c = 63.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-06-28 
  • Released Date: 2019-10-02 
  • Deposition Author(s): Urban, S., Cho, S.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01AI066025

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence