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The crystal structure of GXGD membrane protease FlaK


The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues1,2,3,4. 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 pathogenesis5,6,7, and mutations in presenilin are associated with Alzheimer’s disease8,9,10. 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 related11,12. 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.

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Figure 1: The structure of FlaK.
Figure 2: FlaK is tilted in the membrane.
Figure 3: The uncoupling between Asp 18 and Asp 79.
Figure 4: Structural comparison between FlaK and presenilin-1.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates of FlaK and structure factors have been deposited in the Protein Data Bank under accession code 3S0X.


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We thank A. Héroux, H. Robinson and A. Soares at NSLS, and J. Schuermann at APS NE-CAT for their help during data collection. X-ray diffraction data were measured at beamlines X25 and X29 at NSLS, and at 24-ID-C and 24-ID-E at APS. Financial support was principally from the US Department of Energy and from the National Institutes of Health. This work was supported by a New Scholar Award in Aging from the Ellison Medical Foundation (to Y.H.), a gift from the Neuroscience Education and Research Foundation (to Y.H.) and a pilot grant from Yale’s programme in Cellular Neuroscience, Neurodegeneration, and Repair (CNNR) (to Y.H.).

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Authors and Affiliations



J.H. and Y.X. purified and characterized FlaK in various detergents. J.H. obtained the high-resolution crystals of FlaK. J.H., Y.X. and Y.H. solved the crystal structure. Y.H., Y.X. and J.H. wrote the paper. Y.X. and S.L. screened many constructs and performed the initial biochemical and functional characterizations.

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Correspondence to Ya Ha.

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The authors declare no competing financial interests.

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Hu, J., Xue, Y., Lee, S. et al. The crystal structure of GXGD membrane protease FlaK. Nature 475, 528–531 (2011).

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