Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography
Abstract
Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. Yet, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. Here, we performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. Lastly, these findings shed light on the initial stagemore »
- Authors:
-
[2];
[7];
[7];
[7]
- Nanjing Agricultural Univ., Nanjing (People's Republic of China)
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. of Toledo, Toledo, OH (United States)
- European Spallation Source, Lund (Sweden)
- Technische Univ. Munchen, Garching (Germany)
- Forschungszentrum Julich GmbH, Garching (Germany)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1265915
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Volume: 112; Journal Issue: 40; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences, Washington, DC (United States)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; glycoside hydrolase; protonation state; macromolecular neutron; crystallography; xylanase; molecular simulations
Citation Formats
Wan, Qun, Parks, Jerry M., Hanson, B. Leif, Fisher, Suzanne Zoe, Ostermann, Andreas, Schrader, Tobias E., Graham, David E., Coates, Leighton, Langan, Paul, and Kovalevsky, Andrey. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. United States: N. p., 2015.
Web. doi:10.1073/pnas.1504986112.
Wan, Qun, Parks, Jerry M., Hanson, B. Leif, Fisher, Suzanne Zoe, Ostermann, Andreas, Schrader, Tobias E., Graham, David E., Coates, Leighton, Langan, Paul, & Kovalevsky, Andrey. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. United States. https://doi.org/10.1073/pnas.1504986112
Wan, Qun, Parks, Jerry M., Hanson, B. Leif, Fisher, Suzanne Zoe, Ostermann, Andreas, Schrader, Tobias E., Graham, David E., Coates, Leighton, Langan, Paul, and Kovalevsky, Andrey. Mon .
"Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography". United States. https://doi.org/10.1073/pnas.1504986112. https://www.osti.gov/servlets/purl/1265915.
@article{osti_1265915,
title = {Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography},
author = {Wan, Qun and Parks, Jerry M. and Hanson, B. Leif and Fisher, Suzanne Zoe and Ostermann, Andreas and Schrader, Tobias E. and Graham, David E. and Coates, Leighton and Langan, Paul and Kovalevsky, Andrey},
abstractNote = {Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. Yet, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. Here, we performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. Lastly, these findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.},
doi = {10.1073/pnas.1504986112},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 40,
volume = 112,
place = {United States},
year = {Mon Sep 21 00:00:00 EDT 2015},
month = {Mon Sep 21 00:00:00 EDT 2015}
}
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