Structure-function analysis of Sedolisins: evolution of tripeptidyl peptidase and endopeptidase subfamilies in fungi

Facundo Orts,Arjen Ten Have

doi:10.1186/s12859-018-2404-y

Abstract

BackgroundSedolisins are acid proteases that are related to the basic subtilisins. They have been identified in all three superkingdoms but are not ubiquitous, although fungi that secrete acids as part of their lifestyle can have up to six paralogs. Both TriPeptidyl Peptidase (TPP) and endopeptidase activity have been identified and it has been suggested that these correspond to separate subfamilies.ResultsWe studied eukaryotic sedolisins by computational analysis. A maximum likelihood tree shows one major clade containing non-fungal sequences only and two major as well as two minor clades containing only fungal sequences. One of the major fungal clades contains all known TPPs whereas the other contains characterized endosedolisins. We identified four Cluster Specific Inserts (CSIs) in endosedolisins, of which CSIs 1, 3 and 4 appear as solvent exposed according to structure modeling. Part of CSI2 is exposed but a short stretch forms a novel and partially buried α-helix that induces a conformational change near the binding pocket. We also identified a total of 15 specificity determining positions (SDPs) of which five, identified in two independent analyses, form highly connected SDP sub-networks. Modeling of virtual mutants suggests a key role for the W307A or F307A substitution. The remaining four key SDPs physically interact at the interface of the catalytic domain and the enzyme’s prosegment. Modeling of virtual mutants suggests these SDPs are indeed required to compensate the conformational change induced by CSI2 and the A307. One of the two small fungal clades concerns a subfamily that contains 213 sequences, is mostly similar to the major TPP subfamily but differs, interestingly, in position 307, showing mostly isoleucine and threonine.ConclusionsAnalysis confirms there are at least two sedolisin subfamilies in fungi: TPPs and endopeptidases, and suggests a third subfamily with unknown characteristics. Sequence and functional diversification was centered around buried SDP307 and resulted in a conformational change of the pocket. Mutual Information network analysis forms a useful instrument in the corroboration of predicted SDPs.

Highlights

Sedolisins are acid proteases that are related to the basic subtilisins
Sedolisins are acid proteases related with the basic subtilisins Serine proteases are proteases in which a serine serves as the nucleophylic amino acid in the catalytic site
The catalytic site is most often formed by a triad which can differ among the different unrelated superfamilies

Summary

Introduction

Sedolisins are acid proteases that are related to the basic subtilisins. They have been identified in all three superkingdoms but are not ubiquitous, fungi that secrete acids as part of their lifestyle can have up to six paralogs. Proteases are ubiquitous enzymes that can be classified in many ways Proteases or peptidases degrade proteins by hydrolysis of peptide bonds. They are involved in various biological processes such as cell death [1], nutrition [2] and infections [3]. Sedolisins are acid proteases related with the basic subtilisins Serine proteases are proteases in which a serine serves as the nucleophylic amino acid in the catalytic site. Sedolisins have a calcium binding site albeit at a different position than subtilisins [10]

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