Pretransition state and apo structures of the filamentforming enzyme SgrAI elucidate mechanisms of activation and substrate specificity
AffiliationDepartment of Chemistry and Biochemistry, University of Arizona
Department of Molecular and Cellular Biology, University of Arizona
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CitationShan, Z., Ghadirian, N., Lyumkis, D., & Horton, N. C. (2022). Pretransition state and apo structures of the filamentforming enzyme SgrAI elucidate mechanisms of activation and substrate specificity. Journal of Biological Chemistry.
JournalJournal of Biological Chemistry
RightsCopyright © 2022 the Author(s). Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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AbstractEnzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filamentforming sequence-specific DNA endonuclease SgrAI, the process of filamentation both accelerates its DNA cleavage activity and expands its DNA sequence specificity, thus allowing for many additional DNA sequences to be rapidly cleaved. Both outcomes-the acceleration of DNA cleavage and the expansion of sequence specificity-are proposed to regulate critical processes in bacterial innate immunity. However, the mechanistic bases underlying these events remain unclear. Herein, we describe two new structures of the SgrAI enzyme that shed light on its catalytic function. First, we present the cryo-EM structure of filamentous SgrAI bound to intact primary site DNA and Ca2+ resolved to _2.5 Å within the catalytic center, which represents the trapped enzyme-DNA complex prior to the DNA cleavage reaction. This structure reveals important conformational changes that contribute to the catalytic mechanism and the binding of a second divalent cation in the enzyme active site, which is expected to contribute to increased DNA cleavage activity of SgrAI in the filamentous state. Second, we present an X-ray crystal structure of DNA-free (apo) SgrAI resolved to 2.0 Å resolution, which reveals a disordered loop involved in DNA recognition. Collectively, these multiple new observations clarify the mechanism of expansion of DNA sequence specificity of SgrAI, including the indirect readout of sequence-dependent DNA structure, changes in protein-DNA interactions, and the disorder-to-order transition of a crucial DNA recognition element. © 2022 THE AUTHORS.
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Except where otherwise noted, this item's license is described as Copyright © 2022 the Author(s). Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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