Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.07 kDa 
• Atom Count: 1754 
• Modelled Residue Count: 192 
• Deposited Residue Count: 196 
• Unique protein chains: 1

2NR9

Crystal structure of GlpG, Rhomboid Peptidase from Haemophilus influenzae

• DOI: 10.2210/pdb2NR9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Haemophilus influenzae 86-028NP
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-01 Released: 2006-11-14 
• Deposition Author(s): Lemieux, M.J., Fischer, S.J., Cherney, M.M., Bateman, K.S., James, M.N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.295 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Literature

The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis.

Lemieux, M.J., Fischer, S.J., Cherney, M.M., Bateman, K.S., James, M.N.G.

(2007) Proc Natl Acad Sci U S A 104: 750-754

• PubMed: 17210913 
• DOI: 10.1073/pnas.0609981104
• Primary Citation of Related Structures:  
  2NR9


• PubMed Abstract: 
  

Rhomboid peptidases are members of a family of regulated intramembrane peptidases that cleave the transmembrane segments of integral membrane proteins. Rhomboid peptidases have been shown to play a major role in developmental processes in Drosophila and in mitochondrial maintenance in yeast. Most recently, the function of rhomboid peptidases has been directly linked to apoptosis. We have solved the structure of the rhomboid peptidase from Haemophilus influenzae (hiGlpG) to 2.2-A resolution. The phasing for the crystals of hiGlpG was provided mainly by molecular replacement, by using the coordinates of the Escherichia coli rhomboid (ecGlpG). The structural results on these rhomboid peptidases have allowed us to speculate on the catalytic mechanism of substrate cleavage in a membranous environment. We have identified the relative disposition of the nucleophilic serine to the general base/acid function of the conserved histidine. Modeling a tetrapeptide substrate in the context of the rhomboid structure reveals an oxyanion hole comprising the side chain of a second conserved histidine and the main-chain NH of the nucleophilic serine residue. In both hiGlpG and ecGlpG structures, a water molecule occupies this oxyanion hole.

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Organizational Affiliation: 

Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein glpG homolog	A	196	Haemophilus influenzae 86-028NP	Mutation(s): 2  Gene Names: glpG EC: 3.4.21.105
Find proteins for P44783 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44783  Go to UniProtKB:  P44783

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQE	E [auth A], F [auth A]	3,6,12,15,18,21,24-HEPTAOXAHEXATRIACONTAN-1-OL C29 H60 O8 GEEFJAPPTAALTR-UHFFFAOYSA-N
PA6	B [auth A], C [auth A], D [auth A]	(R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE C9 H17 O8 P JDTMNMAQWVSSOO-MRVPVSSYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.295 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.288	α = 90
b = 35.047	β = 104.02
c = 52.931	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-01 
• Released Date: 2006-11-14 
Deposition Author(s): Lemieux, M.J., Fischer, S.J., Cherney, M.M., Bateman, K.S., James, M.N.G.

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance