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

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. 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.

Authors:
 [1]; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [5]; ORCiD logo [2];  [6]
  1. Univ. of Toledo, Toledo, OH (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Institut Laue Langevin, Grenoble Cedex (France)
  4. Rutherford Appleton Lab., Didcot (United Kingdom)
  5. Univ. of Tennessee, Knoxville, TN (United States)
  6. Univ. of Toledo, Toledo, OH (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1407771
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Dajnowicz, Steven, Johnston, Ryne C., Parks, Jerry M., Blakeley, Matthew P., Keen, David A., Weiss, Kevin L., Gerlits, Oksana, Kovalevsky, Andrey, and Mueser, Timothy C. Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. United States: N. p., 2017. Web. doi:10.1038/s41467-017-01060-y.
Dajnowicz, Steven, Johnston, Ryne C., Parks, Jerry M., Blakeley, Matthew P., Keen, David A., Weiss, Kevin L., Gerlits, Oksana, Kovalevsky, Andrey, & Mueser, Timothy C. Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. United States. doi:10.1038/s41467-017-01060-y.
Dajnowicz, Steven, Johnston, Ryne C., Parks, Jerry M., Blakeley, Matthew P., Keen, David A., Weiss, Kevin L., Gerlits, Oksana, Kovalevsky, Andrey, and Mueser, Timothy C. Mon . "Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme". United States. doi:10.1038/s41467-017-01060-y. https://www.osti.gov/servlets/purl/1407771.
@article{osti_1407771,
title = {Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme},
author = {Dajnowicz, Steven and Johnston, Ryne C. and Parks, Jerry M. and Blakeley, Matthew P. and Keen, David A. and Weiss, Kevin L. and Gerlits, Oksana and Kovalevsky, Andrey and Mueser, Timothy C.},
abstractNote = {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.},
doi = {10.1038/s41467-017-01060-y},
journal = {Nature Communications},
number = 1,
volume = 8,
place = {United States},
year = {Mon Oct 16 00:00:00 EDT 2017},
month = {Mon Oct 16 00:00:00 EDT 2017}
}

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Works referenced in this record:

Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy
journal, January 2005

  • Weigend, Florian; Ahlrichs, Reinhart
  • Physical Chemistry Chemical Physics, Vol. 7, Issue 18, p. 3297-3305
  • DOI: 10.1039/b508541a

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
journal, May 2009

  • Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 18, p. 6378-6396
  • DOI: 10.1021/jp810292n