Protein Synthesis and Degradation
A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome

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Enduring host-microbiome relationships are based on adaptive strategies within a particular ecological niche. Tannerella forsythia is a dysbiotic member of the human oral microbiome that inhabits periodontal pockets and contributes to chronic periodontitis. To counteract endopeptidases from the host or microbial competitors, T. forsythia possesses a serpin-type proteinase inhibitor called miropin. Although serpins from animals, plants, and viruses have been widely studied, those from prokaryotes have received only limited attention. Here we show that miropin uses the serpin-type suicidal mechanism. We found that, similar to a snap trap, the protein transits from a metastable native form to a relaxed triggered or induced form after cleavage of a reactive-site target bond in an exposed reactive-center loop. The prey peptidase becomes covalently attached to the inhibitor, is dragged 75 Å apart, and is irreversibly inhibited. This coincides with a large conformational rearrangement of miropin, which inserts the segment upstream of the cleavage site as an extra β-strand in a central β-sheet. Standard serpins possess a single target bond and inhibit selected endopeptidases of particular specificity and class. In contrast, miropin uniquely blocked many serine and cysteine endopeptidases of disparate architecture and substrate specificity owing to several potential target bonds within the reactive-center loop and to plasticity in accommodating extra β-strands of variable length. Phylogenetic studies revealed a patchy distribution of bacterial serpins incompatible with a vertical descent model. This finding suggests that miropin was acquired from the host through horizontal gene transfer, perhaps facilitated by the long and intimate association of T. forsythia with the human gingiva.

inhibition mechanism
inhibitor
molecular biology
peptidase
periodontal disease
protease
protease inhibitor
protein structure
proteinase
proteolysis

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This work was supported in part by Secretaría de Estado de Investigación, Desarrollo e Innovación Grants BFU2015-64487-R, MDM-2014-0435, and BIO2013-49320-EXP ; Narodowe Centrum Nauki Grants 2015/17/B/NZ1/00666 , “Mobility Plus” 1306/MOB/IV/2015/0, 2012/04/A/NZ1/00051, and 2016/21/B/NZ1/00292; Ministerstwo Nauki i Szkolnictwa Wyższego Grant 2975/7.PR/13/2014/2 ; Seventh Framework Programme Grant FP7-HEALTH-2012-306029-2 “TRIGGER”; Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya Grant 2014SGR9 ; National Institute of Dental and Craniofacial Research, National Institutes of Health Grant R21DE026280 ; Spanish Ministry for Economy and Competitiveness “Juan de la Cierva” Research Contract JCI-2012-13573 (to T. G.); and funding from the European Synchrotron Radiation Facility. The Structural Biology Unit of Molecular Biology Institute of Barcelona is a “María de Maeztu” Unit of Excellence of the Spanish Ministry of Economy, Innovation and Competitiveness. The Faculty of Biochemistry, Biophysics and Biotechnology of the Jagiellonian University is a partner of the Leading National Research Center (KNOW) supported by the Ministry of Science and Higher Education. The authors declare that they have no conflicts of interest with the contents of this article. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

The atomic coordinates and structure factors (codes 5NCS, 5NCT, 5NCU, and 5NCW) have been deposited in the Protein Data Bank (http://wwpdb.org/).

1

Both authors contributed equally to this work.

2

Present address: EMBL Outstation Grenoble, 71 Ave. des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.