Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.37 kDa 
• Atom Count: 1733 
• Modelled Residue Count: 181 
• Deposited Residue Count: 181 
• Unique protein chains: 1

2XOV

Crystal Structure of E.coli rhomboid protease GlpG, native enzyme

• PDB DOI: 10.2210/pdb2XOV/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2010-08-24 Released: 2010-10-13 
• Deposition Author(s): Vinothkumar, K.R., Strisovsky, K., Andreeva, A., Christova, Y., Verhelst, S., Freeman, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.218 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

The structural basis for catalysis and substrate specificity of a rhomboid protease.

Vinothkumar, K.R., Strisovsky, K., Andreeva, A., Christova, Y., Verhelst, S., Freeman, M.

(2010) EMBO J 29: 3797-3809

• PubMed: 20890268 
• DOI: 10.1038/emboj.2010.243
• Primary Citation of Related Structures:  
  2XOV, 2XOW


• PubMed Abstract: 
  

Rhomboids are intramembrane proteases that use a catalytic dyad of serine and histidine for proteolysis. They are conserved in both prokaryotes and eukaryotes and regulate cellular processes as diverse as intercellular signalling, parasitic invasion of host cells, and mitochondrial morphology. Their widespread biological significance and consequent medical potential provides a strong incentive to understand the mechanism of these unusual enzymes for identification of specific inhibitors. In this study, we describe the structure of Escherichia coli rhomboid GlpG covalently bound to a mechanism-based isocoumarin inhibitor. We identify the position of the oxyanion hole, and the S₁- and S₂'-binding subsites of GlpG, which are the key determinants of substrate specificity. The inhibitor-bound structure suggests that subtle structural change is sufficient for catalysis, as opposed to large changes proposed from previous structures of unliganded GlpG. Using bound inhibitor as a template, we present a model for substrate binding at the active site and biochemically test its validity. This study provides a foundation for a structural explanation of rhomboid specificity and mechanism, and for inhibitor design.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHOMBOID PROTEASE GLPG	A	181	Escherichia coli BL21(DE3)	Mutation(s): 0  EC: 3.4.21.105 Membrane Entity: Yes
UniProt
Find proteins for P09391 (Escherichia coli (strain K12)) Explore P09391  Go to UniProtKB:  P09391

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
GOL	U [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.218 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.4	α = 90
b = 110.4	β = 90
c = 127.86	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-24 
• Released Date: 2010-10-13 
Deposition Author(s): Vinothkumar, K.R., Strisovsky, K., Andreeva, A., Christova, Y., Verhelst, S., Freeman, M.

Revision History  

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-02-27
  Changes: Data collection, Database references, Experimental preparation, Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary