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Ligand-Driven Conformational Dynamics Influences Selectivity of UbiX
Szymon Żaczek1, Justyna Kowalska1, Agnieszka Dybala-Defratyka1
1Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland.
Chembiochem : a European Journal of Chemical Biology
|August 24, 2018
Summary
The flavin prenyltransferase UbiX enzyme selectively binds dimethylallyl monophosphate (DMAP) over DMAPP due to its unique conformational dynamics. This enzyme selectivity is crucial for understanding its biological function.
Area of Science:
- Biochemistry
- Enzymology
- Molecular Biology
Background:
- Flavin prenyltransferase UbiX utilizes dimethylallyl monophosphate (DMAP) as a cosubstrate, which is unusual as DMAPP is the common isoprenoid precursor.
- The reason for UbiX's preference for DMAP over DMAPP has remained unclear.
Purpose of the Study:
- To elucidate the molecular mechanism behind UbiX's atypical substrate selectivity for DMAP.
- To investigate the role of enzyme conformational dynamics in substrate recognition.
Main Methods:
- Molecular dynamics (MD) simulations were employed to analyze the interactions between UbiX and its cosubstrates.
- Analysis focused on hydrogen-bonding networks and enzyme conformational changes.
Main Results:
- UbiX's hydrogen-bonding network does not adequately accommodate DMAPP, leading to significant enzyme conformational changes and unreactive trajectories.
- DMAP consistently maintains a catalytically competent position within the enzyme throughout the simulations.
- Conformational dynamics of UbiX are identified as the key determinant of its substrate selectivity.
Conclusions:
- The study provides a mechanistic explanation for UbiX's preference for DMAP.
- Enzyme conformational dynamics play a critical role in governing the substrate specificity of flavin prenyltransferases.
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