Hyoscyamine 6β-hydroxylase (H6H) is a bifunctional non-heme 2-oxoglutarate/Fe2+-dependent dioxygenase that catalyzes the two final steps in the biosynthesis of scopolamine. Based on high resolution crystal structures of H6H from Datura metel, detailed information on substrate binding was obtained that provided insights into the onset of the enzymatic process. In particular, the role of two prominent residues was revealed - Glu-116 that interacts with the tertiary amine located on the hyoscyamine tropane moiety and Tyr-326 that forms CH-π hydrogen bonds with the hyoscyamine phenyl ring. The structures were used as the basis for QM/MM calculations that provided an explanation for the regioselectivity of the hydroxylation reaction on the hyoscyamine tropane moiety (C6 vs. C7) and quantified contributions of active site residues to respective barrier heights.
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http://dx.doi.org/10.1039/d0dt00302f | DOI Listing |
J Am Chem Soc
January 2025
Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany, 45470.
Molybdenum nitrogenase plays a crucial role in the biological nitrogen cycle by catalyzing the reduction of dinitrogen (N) to ammonia (NH) under ambient conditions. However, the underlying mechanisms of nitrogenase catalysis, including electron and proton transfer dynamics, remain only partially understood. In this study, we covalently attached molybdenum nitrogenase (MoFe) to gold electrodes and utilized surface-enhanced infrared absorption spectroscopy (SEIRA) coupled with electrochemistry techniques to investigate its catalytic mechanism.
View Article and Find Full Text PDFmLife
December 2024
Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering, East China Normal University Shanghai China.
In silico computational methods have been widely utilized to study enzyme catalytic mechanisms and design enzyme performance, including molecular docking, molecular dynamics, quantum mechanics, and multiscale QM/MM approaches. However, the manual operation associated with these methods poses challenges for simulating enzymes and enzyme variants in a high-throughput manner. We developed the NAC4ED, a high-throughput enzyme mutagenesis computational platform based on the "near-attack conformation" design strategy for enzyme catalysis substrates.
View Article and Find Full Text PDFProtein Sci
January 2025
Departament de Química, Universitat Autònoma de Barcelona, Barcelona, Spain.
Cyclooxygenase-2 (COX-2) plays a crucial role in inflammation and has been implicated in cancer development. Understanding the behavior of COX-2 in different cellular contexts is essential for developing targeted therapeutic strategies. In this study, we investigate the fluorescence spectrum of a fluorogenic probe, NANQ-IMC6, when bound to the active site of human COX-2 in both its monomeric and homodimeric forms.
View Article and Find Full Text PDFJ Phys Chem B
December 2024
Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4.
Despite the remarkable resistance of the nucleic acid phosphodiester backbone to degradation affording genetic stability, the P-O bond must be broken during DNA repair and RNA metabolism, among many other critical cellular processes. Nucleases are powerful enzymes that can enhance the uncatalyzed rate of phosphodiester bond cleavage by up to ∼10-fold. Despite the most well accepted hydrolysis mechanism involving two metals (M to activate a water nucleophile and M to stabilize the leaving group), experimental evidence suggests that some nucleases can use a single metal to facilitate the chemical step, a controversial concept in the literature.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy.
We present a polarizable embedding quantum mechanics/molecular mechanics (QM/MM) framework for ground- and excited-state Complete Active Space Self-Consistent Field (CASSCF) calculations on molecules within complex environments, such as biological systems. These environments are modeled using the AMOEBA polarizable force field. This approach is implemented by integrating the OpenMMPol library with the CFour quantum chemistry software suite.
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