A structural investigation of novel fungal polyglycine hydrolases

Abstract

Polyglycine hydrolases (PGH) are a family of fungal proteases that are known to cleave the polyglycine linker of Zea mays chitinase, ChitA, thwarting one mechanism of plant defense against fungal infection. Previously, little was known at the atomic level about the interaction between these proteases and their target. There has been limited biochemical characterization and no structural characterization of this family of proteases. In this work, we analyze the atomic structure of one of these polyglycine hydrolases, Fvan-cmp. The structure was solved by X-ray crystallography using a de novo RoseTTAFold model. We report models for the other identified polyglycine hydrolases utilizing the previously determined structure, as well as insights into features likely involved in the catalytic mechanism. The PGH structural characterization identified a two-domain structure, simply named N- and C- domain. The N-domain is a novel tertiary fold found throughout all kingdoms but functionally unidentified. The C-domain shares structural similarities with Class C β-lactamases including the conserved active site motifs and catalytic residues. Utilizing a combination of in vitro and in silico methods, we propose a PGH-ChitA complex model that is supported by previous understanding of PGHs and the structural data. Throughout this work, we discuss the merits and limitations of current in silico methods with a focus on de novo protein modelling and protein-protein docking methods.