Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme

Steven Dajnowicz, Ryne C. Johnston, Jerry M. Parks, Matthew P. Blakeley, David A. Keen, Kevin L. Weiss, Oksana Gerlits, Andrey Kovalevsky () and Timothy C. Mueser ()
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Steven Dajnowicz: University of Toledo
Ryne C. Johnston: Oak Ridge National Laboratory
Jerry M. Parks: Oak Ridge National Laboratory
Matthew P. Blakeley: Institut Laue Langevin
David A. Keen: Rutherford Appleton Laboratory
Kevin L. Weiss: Oak Ridge National Laboratory
Oksana Gerlits: University of Tennessee
Andrey Kovalevsky: Oak Ridge National Laboratory
Timothy C. Mueser: University of Toledo

Nature Communications, 2017, vol. 8, issue 1, 1-9

Abstract: Abstract Enzymes dependent on pyridoxal 5′-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase.

Date: 2017
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DOI: 10.1038/s41467-017-01060-y

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