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The structural basis for catalysis and substrate specificity of a rhomboid protease

DOI: 10.1038/emboj.2010.243 DOI Help
PMID: 20890268 PMID Help

Authors: Kutti R. Vinothkumar (MRC Laboratory of Molecular Biology) , Kvido Strisovsky (MRC Laboratory of Molecular Biology) , Antonina Andreeva (MRC Laboratory of Molecular Biology) , Yonka Christova (MRC Laboratory of Molecular Biology) , Steven Verhelst (Technische Universit√§t M√ľnchen) , Matthew Freeman (MRC Laboratory of Molecular Biology)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: The Embo Journal

State: Published (Approved)
Published: September 2010

Abstract: Rhomboids are intramembrane proteases that use a catalytic dyad of serine and histidine for proteolysis. They are conserved in both prokaryotes and eukaryotes and regulate cellular processes as diverse as intercellular signalling, parasitic invasion of host cells, and mitochondrial morphology. Their widespread biological significance and consequent medical potential provides a strong incentive to understand the mechanism of these unusual enzymes for identification of specific inhibitors. In this study, we describe the structure of Escherichia coli rhomboid GlpG covalently bound to a mechanism?based isocoumarin inhibitor. We identify the position of the oxyanion hole, and the S1? and S2??binding subsites of GlpG, which are the key determinants of substrate specificity. The inhibitor?bound structure suggests that subtle structural change is sufficient for catalysis, as opposed to large changes proposed from previous structures of unliganded GlpG. Using bound inhibitor as a template, we present a model for substrate binding at the active site and biochemically test its validity. This study provides a foundation for a structural explanation of rhomboid specificity and mechanism, and for inhibitor design.

Journal Keywords: Crystallography; X-Ray; DNA-Binding; Endopeptidases; Enzyme; Escherichia; Isocoumarins; Membrane; Models; Molecular; Mutation; Protein; Substrate Specificity

Subject Areas: Biology and Bio-materials


Instruments: I02-Macromolecular Crystallography , I03-Macromolecular Crystallography , I04-Macromolecular Crystallography

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