Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model

Authors: DOWLING, NICOLE - University Of Waterloo; Naumann, Todd; Price, Neil; ROSE, DAVID - University Of Waterloo

Submitted to: Acta Crystallographica, Section D: Biological Crystallography
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/11/2023
Publication Date: 1/1/2023
Citation: Dowling, N.V., Naumann, T.A., Price, N.P.J., Rose, D.R. 2023. Crystal structure of a polyglycine hydrolase determined using a RoseTTAFold model. Acta Crystallographica, Section D: Structural Biology. 79:168-176. https://doi.org/10.1107/S2059798323000311.
DOI: https://doi.org/10.1107/S2059798323000311

Interpretive Summary: Fungal pathogens secrete enzymes that can break down plant defense proteins. These fungal enzymes called, polyglycine hydrolases, have two parts. One part is similar to bacterial proteins that reduce antibiotic activity. The other part is unlike any other known protein. ARS researchers in Peoria, Illinois, working with researchers in Waterloo, Ontario, Canada, determined the 3-dimensional structure of two parts using X-ray crystallography. Seeing how the two parts of the enzyme fit together in space allows for understanding how the enzyme works, and how it can be stopped from breaking down plant defense proteins. Additionally, using new artificial intelligence computational methods, they were able to find other fungal proteins with similar structure using genomic sequence information. Although the sequence information was very different the 3-dimensional structures were similar. These discoveries have helped identify new enzymes that fungal pathogens use to cause disease. This information will help develop methods to improved disease resistance and reduce crop losses.

Technical Abstract: Polyglycine hydrolases (PGHs) are secreted fungal proteases that cleave the polyglycine linker of Zea mays ChitA, a defensive chitinase, thus overcoming one mechanism of plant resistance to infection. Despite their importance in agriculture, there has been no previous structural characterization of this family of proteases. The objective of this research was to investigate the proteolytic mechanism and other characteristics by structural and biochemical means. Here, the first atomic structure of a polyglycine hydrolase was identified. It was solved by X-ray crystallography using a RoseTTAFold model, taking advantage of recent technical advances in structure prediction. PGHs are composed of two domains: the N- and C-domains. The N-domain is a novel tertiary fold with an as-yet unknown function that is found across all kingdoms of life. The C-domain shares structural similarities with class C ß-lactamases, including a common catalytic nucleophilic serine. In addition to insights into the PGH family and its relationship to ß-lactamases, the results demonstrate the power of complementing experimental structure determination with new computational techniques.