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Title: Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme

Journal Article · · Nature Communications

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. As a result, 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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1407771
Journal Information:
Nature Communications, Vol. 8, Issue 1; ISSN 2041-1723
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

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Dimerization misalignment in human glutamate-oxaloacetate transaminase variants is the primary factor for PLP release journal September 2018
Neutron scattering in the biological sciences: progress and prospects journal December 2018
Instrument and shielding design of a neutron diffractometer at J-PARC for protein crystallography covering crystals with large unit-cell volume journal April 2018
Current Advances on Structure-Function Relationships of Pyridoxal 5′-Phosphate-Dependent Enzymes journal March 2019
Hyperconjugation promoted by hydrogen bonding between His98/His241 and a carboxyl group contributes to tyrosine decarboxylase catalysis journal January 2019
Neutron macromolecular crystallography journal February 2018
Neutron Macromolecular Crystallography book January 2020
Current Advances on Structure-Function Relationships of Pyridoxal 5′-Phosphate-Dependent Enzymes journal March 2019
Dimerization misalignment in human glutamate-oxaloacetate transaminase variants is the primary factor for PLP release journal September 2018

Figures / Tables (8)