Document Type
Article
Publication Date
8-2023
Publication Title
Protein Science
Volume
32
Issue
8
Pages
1-16
Publisher Name
Wiley Periodicals LLC
Abstract
An increased understanding of how the acceptor site in Gcn5-related N-acetyltransferase (GNAT) enzymes recognizes various substrates provides important clues for GNAT functional annotation and their use as chemical tools. In this study, we explored how the PA3944 enzyme from Pseudomonas aeruginosa recognizes three different acceptor substrates, including aspartame, NANMO, and polymyxin B, and identified acceptor residues that are critical for substrate specificity. To achieve this, we performed a series of molecular docking simulations and tested methods to identify acceptor substrate binding modes that are catalytically relevant. We found that traditional selection of best docking poses by lowest S scores did not reveal acceptor substrate binding modes that were generally close enough to the donor for productive acetylation. Instead, sorting poses based on distance between the acceptor amine nitrogen atom and donor carbonyl carbon atom placed these acceptor substrates near residues that contribute to substrate specificity and catalysis. To assess whether these residues are indeed contributors to substrate specificity, we mutated seven amino acid residues to alanine and determined their kinetic parameters. We identified several residues that improved the apparent affinity and catalytic efficiency of PA3944, especially for NANMO and/or polymyxin B. Additionally, one mutant (R106A) exhibited substrate inhibition toward NANMO, and we propose scenarios for the cause of this inhibition based on additional substrate docking studies with R106A. Ultimately, we propose that this residue is a key gatekeeper between the acceptor and donor sites by restricting and orienting the acceptor substrate within the acceptor site.
Recommended Citation
Variot, Cillian; Capule, Daniel; Arolli, Xhulio; Baumgartner, Jackson; Reidl, Cory T.; Houseman, Charles; Ballicora, Miguel; Becker, Daniel P. Ph.D.; and Kuhn, Misty L.. Mapping Roles of Active Site Residues in the Acceptor Site of the PA3944 Gcn5-Related N-Acetyltransferase Enzyme. Protein Science, 32, 8: 1-16, 2023. Retrieved from Loyola eCommons, Chemistry: Faculty Publications and Other Works, http://dx.doi.org/10.1002/pro.4725
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Copyright Statement
© The Protein Society, 2023.
Comments
Author Posting © The Protein Society, 2023. This is the peer reviewed version of the following article: Variot C, Capule D, Arolli X, Baumgartner J, Reidl C, Houseman C, et al. Mapping roles of active site residues in the acceptor site of the PA3944 Gcn5-related N-acetyltransferase enzyme. Protein Science. 2023; 32(8):e4725, which has been published in final form at https://doi.org/10.1002/pro.4725. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited.