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Journal Article

The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase


Wagner,  Tristan
Research Group Microbial Metabolism, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Huang, G., Wagner, T., Demmer, U., Warkentin, E., Ermler, U., & Shima, S. (2020). The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase. Journal of Molecular Biology (London), 432(7), 2042-2054. doi:10.1016/j.jmb.2020.01.042.

Cite as: https://hdl.handle.net/21.11116/0000-0007-F1DB-2
NADP-dependent methylene-tetrahydromethanopterin (methylene-H4MPT)
dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of
methylene-H4MPT to form methenyl-H4MPT+ by using NADP(+) as a hydride
acceptor. This hydride transfer reaction is involved in the oxidative
metabolism from formaldehyde to CO2 in methylotrophic and methanotrophic
bacteria. Here, we report on the crystal structures of the ternary
MtdA-substrate complexes from Methylorubrum extorquens AM1 obtained in
open and closed forms. Their conversion is accomplished by
opening/closing the active site cleft via a 15 degrees rotation of the
NADP, relative to the pterin domain. The 1.08 angstrom structure of the
closed and active enzyme-NADP-methylene-H4MPT complex allows a detailed
geometric analysis of the bulky substrates and a precise prediction of
the hydride trajectory. Upon domain closure, the bulky substrate rings
become compressed resulting in a tilt of the imidazolidine group of
methylene-H4MPT that optimizes the geometry for hydride transfer. An
additional 1.5 A structure of MtdA in complex with the nonreactive
NADP(+) and methenyl-H4MPT+ revealed an extremely short distance between
nicotinamide-C4 and imidazoline-C14a of 2.5 angstrom, which demonstrates
the strong pressure imposed. The pterin-imidazolidine-phenyl butterfly
angle of methylene-H4MPT bound to MtdA is smaller than that in the
enzyme-free state but is similar to that in H-2- and F-420-dependent
methylene-H4MPT dehydrogenases. The concept of compression-driven
hydride transfer including quantum mechanical hydrogen tunneling
effects, which are established for flavin- and NADP-dependent enzymes,
can be expanded to hydride-transferring H4MPT-dependent enzymes. (C)
2020 Elsevier Ltd. All rights reserved.