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Lookup NU author(s): Heli Monttinen
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© 2019 Mönttinen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Specific cleavage of proteins by proteases is essential for several cellular, physiological, and viral processes. Chymotrypsin-related proteases that form the PA clan in the MEROPS classification of proteases is one of the largest and most diverse group of proteases. The PA clan comprises serine proteases from bacteria, eukaryotes, archaea, and viruses and chymotrypsin-related cysteine proteases from positive-strand RNA viruses. Despite low amino acid sequence identity, all PA clan proteases share a conserved double β-barrel structure. Using an automated structure-based hierarchical clustering method, we identified a common structural core of 72 amino acid residues for 143 PA clan proteases that represent 12 protein families and 11 subfamilies. The identified core is located around the catalytic site between the two β-barrels and resembles the structures of the smallest PA clan proteases. We constructed a structure-based distance tree derived from the properties of the identified common core. Our structure-based analyses support the current classification of these proteases at the subfamily level and largely at the family level. Structural alignment and structure-based distance trees could thus be used for directing objective classification of PA clan proteases and to strengthen their higher order classification. Our results also indicate that the PA clan proteases of positive-strand RNA viruses are related to cellular heatshock proteases, which suggests that the exchange of protease genes between viruses and cells might have occurred more than once.
Author(s): Monttinen HAM, Ravantti JJ, Poranen MM
Publication type: Article
Publication status: Published
Journal: PLoS ONE
Year: 2019
Volume: 14
Issue: 5
Online publication date: 17/05/2019
Acceptance date: 25/04/2019
Date deposited: 13/06/2019
ISSN (electronic): 1932-6203
Publisher: Public Library of Science
URL: https://doi.org/10.1371/journal.pone.0216659
DOI: 10.1371/journal.pone.0216659
PubMed id: 31100077
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