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Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry

Nature Structural & Molecular Biology volume 13, pages 1084–1091 (2006)Cite this article

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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Figure 1: Overall structure of the transmembrane core domain of GlpG, an E. coli intramembrane protease of the rhomboid family.
Figure 2: Sequence alignment of rhomboid homologs in diverse species.
Figure 3: Conformation of the active site and the L1 loop.
Figure 4: Mechanisms of water access and substrate entry to the active site.
Figure 5: A proposed model of action for the rhomboid family of intramembrane proteases.
Figure 6: A proposed general mechanism for intramembrane proteases.

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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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Author notes

  1. Zhuoru Wu, Nieng Yan and Liang Feng: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, 08544, New Jersey, USA

    Zhuoru Wu, Nieng Yan, Liang Feng, Adam Oberstein, Hanchi Yan, Philip D Jeffrey & Yigong Shi

  2. Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USA

    Rosanna P Baker & Sinisa Urban

  3. State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China

    Lichuan Gu

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Contributions

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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Correspondence to Yigong Shi.

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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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