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Li Z, Zhang X, Wang Q, Li C, Zhang N, Zhang X, Xu B, Ma B, Schrader TE, Coates L, Kovalevsky A, Huang Y, Wan Q. Understanding the pH-Dependent Reaction Mechanism of a Glycoside Hydrolase Using High-Resolution X-ray and Neutron Crystallography. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01472] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Xiaoshuai Zhang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Qingqing Wang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Chunran Li
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Nianying Zhang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Xinkai Zhang
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Birui Xu
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Baoliang Ma
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Tobias E. Schrader
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Garching 85747, Germany
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, People’s Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
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Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Proc Natl Acad Sci U S A 2015; 112:12384-9. [PMID: 26392527 DOI: 10.1073/pnas.1504986112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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. However, 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. 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. 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.
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Wan Q, Kovalevsky A, Zhang Q, Hamilton-Brehm S, Upton R, Weiss KL, Mustyakimov M, Graham D, Coates L, Langan P. Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:320-3. [PMID: 23519813 PMCID: PMC3606583 DOI: 10.1107/s1744309113001164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 01/11/2013] [Indexed: 11/10/2022]
Abstract
Xylanase II from Trichoderma reesei catalyzes the hydrolysis of glycosidic bonds in xylan. Crystallographic studies of this commercially important enzyme have been initiated to investigate its reaction mechanism, substrate binding and dependence on basic pH conditions. The wild-type protein was heterologously expressed in an Escherichia coli host using the defined medium and four active-site amino acids were replaced to abolish its activity (E177Q and E86Q) or to change its pH optimum (N44D and N44H). Cation-exchange and size-exclusion chromatography were used to obtain >90% protein purity. The ligand-free proteins and variant complexes containing substrate (xylohexaose) or product (xylotriose) were crystallized in several different space groups and diffracted to high resolutions (from 1.07 to 1.55 Å).
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Affiliation(s)
- Qun Wan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Qiu Zhang
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Scott Hamilton-Brehm
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Rosalynd Upton
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kevin L. Weiss
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Marat Mustyakimov
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - David Graham
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Paul Langan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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Einspahr H, Weiss MS. Crystals on the cover 2012. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1. [PMID: 22232160 PMCID: PMC3253823 DOI: 10.1107/s1744309111053759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 12/23/2011] [Indexed: 11/10/2022]
Abstract
Editorial.
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Affiliation(s)
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (BESSY-MX), Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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