3S0X

The crystal structure of GxGD membrane protease FlaK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.276 

wwPDB Validation 3D Report Full Report



Literature

The crystal structure of GXGD membrane protease FlaK.

Hu, J.Xue, Y.Lee, S.Ha, Y.

(2011) Nature 475: 528-531

  • DOI: 10.1038/nature10218
  • Primary Citation of Related Structures:  
    3S0X

  • PubMed Abstract: 
  • The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase ...

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 Å resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.


    Organizational Affiliation

    Department of Pharmacology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidase A24B, FlaK domain proteinAB237Methanococcus maripaludisMutation(s): 0 
Gene Names: MmarC6_0338
EC: 3.4.23.52
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Intramembrane Proteases
Protein: 
FlaK preflagellin aspartyl protease
Find proteins for A9A677 (Methanococcus maripaludis (strain C6 / ATCC BAA-1332))
Explore A9A677 
Go to UniProtKB:  A9A677
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.276 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.895α = 90
b = 99.715β = 90
c = 118.436γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
SHELXSphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-05-13 
  • Released Date: 2011-08-03 
  • Deposition Author(s): Hu, J., Xue, Y., Ha, Y.

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release