Abstract
Intramembrane proteolysis regulates diverse biological processes. Cleavage of substrate peptide bonds within the membrane bilayer is catalyzed by integral membrane proteases. Here we report the crystal structure of the transmembrane core domain of GlpG, a rhomboid-family intramembrane serine protease from Escherichia coli. The protein contains six transmembrane helices, with the catalytic Ser201 located at the N terminus of helix α4 approximately 10 Å below the membrane surface. Access to water molecules is provided by a central cavity that opens to the extracellular region and converges on Ser201. One of the two GlpG molecules in the asymmetric unit has an open conformation at the active site, with the transmembrane helix α5 bent away from the rest of the molecule. Structural analysis suggests that substrate entry to the active site is probably gated by the movement of helix α5.
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Acknowledgements
We thank A. Saxena at Brookhaven National Laboratory National Synchrotron Light Source beamlines for help, J. Chai and Q. Liu for technical discussion and Y. Ha (Yale University) for the atomic coordinates of GlpG. This work was supported by Princeton University (Y.S.). Work in the Urban laboratory is supported by US National Institutes of Health grant 1R01AI066025 and a Career Award in the Biomedical Sciences from the Burroughs-Wellcome Fund (to S.U.).
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Z.W., N.Y., L.F., A.O. and H.Y. contributed to the design and execution of the structural biology project. R.P.B. and S.U. contributed to the enzymatic characterization of GlpG. Z.W., N.Y. and P.D.J. contributed to data collection. L.G. contributed to structure refinement. Y.S. contributed to overall guidance of the project and manuscript preparation. Z.W., N.Y., L.F. and S.U. commented on the manuscript.
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Supplementary information
Supplementary Video 1
Comparison of GlpG structure in the closed state (ref. 24) with that in the open state (molecule A). GlpG structure in the closed state (ref. 24) is viewed from the top (video 1) or the side (video 2) of the active-site cavity in the two videos. The putative catalytic dyad residues Ser201 and His254 are shown. The GlpG structure shown half-way through the video is the open state (molecule A). Note the large conformational changes in the transmembrane helix α5 and the L5 loop between the closed and open states of GlpG. (MPG 3230 kb)
Supplementary Video 2
Comparison of GlpG structure in the closed state (ref. 24) with that in the open state (molecule A). GlpG structure in the closed state (ref. 24) is viewed from the top (video 1) or the side (video 2) of the active-site cavity in the two videos. The putative catalytic dyad residues Ser201 and His254 are shown. The GlpG structure shown half-way through the video is the open state (molecule A). Note the large conformational changes in the transmembrane helix α5 and the L5 loop between the closed and open states of GlpG. (MPG 3129 kb)
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Wu, Z., Yan, N., Feng, L. et al. Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry. Nat Struct Mol Biol 13, 1084–1091 (2006). https://doi.org/10.1038/nsmb1179
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DOI: https://doi.org/10.1038/nsmb1179
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