Structural and functional insights into Escherichia coli α2-macroglobulin endopeptidase snap-trap inhibition

This article contains supporting information online (a detailed description of the experimental procedures is provided in the SI Appendix. The latter also includes four supplementary tables, 10 supplementary figures, the Acknowledgments, and SI Appendix, SRD.) at http://www.pnas.org/content/suppl/2015/06/19/1506538112.DCSupplemental/pnas.1506538112.sapp.pdf
The survival of commensal bacteria requires them to evade host peptidases. Gram-negative bacteria from the human gut microbiome encode a relative of the human endopeptidase inhibitor, α2 -macroglobulin (α2 M). Escherichia coli α2 M (ECAM) is a ∼180-kDa multidomain membrane-anchored pan-peptidase inhibitor, which is cleaved by host endopeptidases in an accessible bait region. Structural studies by electron microscopy and crystallography reveal that this cleavage causes major structural rearrangement of more than half the 13-domain structure from a native to a compact induced form. It also exposes a reactive thioester bond, which covalently traps the peptidase. Subsequently, peptidase-laden ECAM is shed from the membrane and may dimerize. Trapped peptidases are still active except against very large substrates, so inhibition potentially prevents damage of large cell envelope components, but not host digestion. Mechanistically, these results document a novel monomeric >snap trap.>.
This study was supported in part by grants from public and private agencies from the European Community, Spain, and Catalonia (FP7-PEOPLE-2011-ITN-290246 “RAPID,” FP7-HEALTH-2012-306029-2 “TRIGGER;” BFU2011-25902, BFU2012-32862, BIO2013-49320-EXP, MDM-2014-0435; and 2014SGR9) and an FPU Ph.D. fellowship (AP2010-3799) from the Spanish Ministry for Education, Culture and Sport to I.G.-F. The Department of Structural Biology of IBMB is a “María de Maeztu” Unit of Excellence from the Ministry of Economy and Competitiveness. We acknowledge the help provided by ESRF and ALBA synchrotron local contacts. Funding for travelling and synchrotron data collection was provided in part by ESRF