2IRV

Crystal structure of GlpG, a rhomboid intramembrane serine protease

• PDB DOI: https://doi.org/10.2210/pdb2IRV/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2006-10-16 Released: 2006-10-31 
• Deposition Author(s): Bibi, E., Fass, D., Ben-Shem, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.220 

Literature

Structural basis for intramembrane proteolysis by rhomboid serine proteases.

Ben-Shem, A., Fass, D., Bibi, E.

(2007) Proc Natl Acad Sci U S A 104: 462-466

• PubMed: 17190827 
• DOI: https://doi.org/10.1073/pnas.0609773104
• Primary Citation of Related Structures:  
  2IRV


• PubMed Abstract: 
  

  Intramembrane proteases catalyze peptide bond cleavage of integral membrane protein substrates. This activity is crucial for many biological and pathological processes. Rhomboids are evolutionarily widespread intramembrane serine proteases. Here, we present the 2.3-A-resolution crystal structure of a rhomboid from Escherichia coli. The enzyme has six transmembrane helices, five of which surround a short TM4, which starts deep within the membrane at the catalytic serine residue. Thus, the catalytic serine is in an externally exposed cavity, which provides a hydrophilic environment for proteolysis. Our results reveal a mechanism to enable water-dependent catalysis at the depth of the hydrophobic milieu of the membrane and suggest how substrates gain access to the sequestered rhomboid active site.

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Organizational Affiliation: 

Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.38 kDa 
• Atom Count: 3,196 
• Modelled Residue Count: 355 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein glpG	A, B	182	Escherichia coli K-12	Mutation(s): 0  Gene Names: glpG Membrane Entity: Yes
UniProt
Find proteins for P09391 (Escherichia coli (strain K12)) Explore P09391  Go to UniProtKB:  P09391

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGV	U [auth B], V [auth B], W [auth B], X [auth B]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C40 H77 O10 P ADYWCMPUNIVOEA-GPJPVTGXSA-N
LMT	T [auth B]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
PO4	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.263 
• R-Value Work: 0.220 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.82	α = 90
b = 69.35	β = 101.03
c = 67.58	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): Bibi, E., Fass, D., Ben-Shem, A.

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Structure summary