Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase

Mueser, Timothy; Drago, Victoria; Kovalevsky, Andrii Y.; Dajnowicz, Steven

doi:10.1016/bs.mie.2020.01.009

Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase

Journal Article · Sat Feb 01 00:00:00 EST 2020 · Methods in Enzymology

DOI:https://doi.org/10.1016/bs.mie.2020.01.009· OSTI ID:1606038

Mueser, Timothy ^[1]; Drago, Victoria ^[1]; ^[2]; Dajnowicz, Steven ^[1]

Univ. of Toledo, OH (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1606038

Journal Information:: Methods in Enzymology, Journal Name: Methods in Enzymology Journal Issue: 1 Vol. 634; ISSN 0076-6879

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (37)

Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site Gerlits, Oksana; Wymore, Troy; Das, Amit Angewandte Chemie International Edition, Vol. 55, Issue 16 https://doi.org/10.1002/anie.201509989	journal	March 2016
Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. Hendrickson, W. A.; Horton, J. R.; LeMaster, D. M. The EMBO Journal, Vol. 9, Issue 5 https://doi.org/10.1002/j.1460-2075.1990.tb08287.x	journal	May 1990
Very fast prediction and rationalization of pKa values for protein-ligand complexes Bas, Delphine C.; Rogers, David M.; Jensen, Jan H. Proteins: Structure, Function, and Bioinformatics, Vol. 73, Issue 3 https://doi.org/10.1002/prot.22102	journal	May 2008
Progress in the prediction of pKa values in proteins Alexov, Emil; Mehler, Ernest L.; Baker, Nathan Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 12 https://doi.org/10.1002/prot.23189	journal	October 2011
The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins Nielsen, Jens E.; Gunner, M. R.; García-Moreno E., Bertrand Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 12 https://doi.org/10.1002/prot.23194	journal	October 2011
The quantum chemical cluster approach for modeling enzyme reactions: The quantum chemical cluster approach Siegbahn, Per E. M.; Himo, Fahmi Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 3 https://doi.org/10.1002/wcms.13	journal	March 2011
Preliminary crystallographic study of aspartate: 2-oxoglutarate aminotransferase from pig heart Arnone, Arthur; Rogers, Paul H.; Schmidt, Jane Journal of Molecular Biology, Vol. 112, Issue 3 https://doi.org/10.1016/S0022-2836(77)80196-4	journal	May 1977
Structure, evolution and action of vitamin B6-dependent enzymes Jansonius, Johan N. Current Opinion in Structural Biology, Vol. 8, Issue 6 https://doi.org/10.1016/S0959-440X(98)80096-1	journal	December 1998
Strain and catalysis in aspartate aminotransferase Hayashi, Hideyuki; Mizuguchi, Hiroyuki; Miyahara, Ikuko Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1647, Issue 1-2 https://doi.org/10.1016/S1570-9639(03)00068-2	journal	April 2003
Aspartate aminotransferase: An old dog teaches new tricks Toney, Michael D. Archives of Biochemistry and Biophysics, Vol. 544 https://doi.org/10.1016/j.abb.2013.10.002	journal	February 2014
Controlling reaction specificity in pyridoxal phosphate enzymes Toney, Michael D. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1814, Issue 11 https://doi.org/10.1016/j.bbapap.2011.05.019	journal	November 2011
Hyperconjugation Promotes Catalysis in a Pyridoxal 5′-Phosphate-Dependent Enzyme Dajnowicz, Steven; Parks, Jerry M.; Hu, Xiche ACS Catalysis, Vol. 8, Issue 7 https://doi.org/10.1021/acscatal.8b01911	journal	May 2018
Reaction of Aspartate Aminotransferase with L-erythro-3-Hydroxyaspartate: Involvement of Tyr70 in Stabilization of the Catalytic Intermediates Hayashi, Hideyuki; Kagamiyama, Hiroyuki Biochemistry, Vol. 34, Issue 29 https://doi.org/10.1021/bi00029a017	journal	July 1995
Crystal Structure of a D-Amino Acid Aminotransferase: How the Protein Controls Stereoselectivity Sugio, Shigetoshi; Petsko, Gregory A.; Manning, James M. Biochemistry, Vol. 34, Issue 30 https://doi.org/10.1021/bi00030a002	journal	August 1995
2.8-.ANG.-resolution crystal structure of an active-site mutant of aspartate aminotransferase from Escherichia coli Smith, Douglas L.; Almo, Steven C.; Toney, Michael D. Biochemistry, Vol. 28, Issue 20 https://doi.org/10.1021/bi00446a030	journal	October 1989
Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology van der Kamp, Marc W.; Mulholland, Adrian J. Biochemistry, Vol. 52, Issue 16 https://doi.org/10.1021/bi400215w	journal	April 2013
Exchange of K ⁺ or Cs ⁺ for Na ⁺ Induces Local and Long-Range Changes in the Three-Dimensional Structure of the Tryptophan Synthase α ₂ β ₂ Complex ^‡ Rhee, Sangkee; Parris, Kevin D.; Ahmed, S. Ashraf Biochemistry, Vol. 35, Issue 13 https://doi.org/10.1021/bi952506d	journal	January 1996
Determination of the Structure of Alanine Racemase from Bacillus stearothermophilus at 1.9-Å Resolution ^† ^, ^‡ Shaw, Jeffrey P.; Petsko, Gregory A.; Ringe, Dagmar Biochemistry, Vol. 36, Issue 6 https://doi.org/10.1021/bi961856c	journal	February 1997
Transient-State Kinetics of the Reaction of Aspartate Aminotransferase with Aspartate at Low pH Reveals Dual Routes in the Enzyme−Substrate Association Process ^† Hayashi, Hideyuki; Kagamiyama, Hiroyuki Biochemistry, Vol. 36, Issue 44 https://doi.org/10.1021/bi971638z	journal	November 1997
Semiempirical calculations of the electronic absorption spectra of vitamin B6 derivatives in the active site of mitochondrial aspartate aminotransferase Clark, P. A.; Jansonius, J. N.; Mehler, E. L. Journal of the American Chemical Society, Vol. 115, Issue 5 https://doi.org/10.1021/ja00058a039	journal	March 1993
Semiempirical calculations of the electronic absorption spectrum of mitochondrial aspartate aminotransferase. 2. The 2-methylaspartate complex Clark, P. A.; Jansonius, J. N.; Mehler, E. L. Journal of the American Chemical Society, Vol. 115, Issue 21 https://doi.org/10.1021/ja00074a053	journal	October 1993
Equilibriums and absorption spectra of Schiff bases Metzler, Carol M.; Cahill, Allen; Metzler, David E. Journal of the American Chemical Society, Vol. 102, Issue 19 https://doi.org/10.1021/ja00539a017	journal	September 1980
Role of the Pyridine Nitrogen in Pyridoxal 5′-Phosphate Catalysis: Activity of Three Classes of PLP Enzymes Reconstituted with Deazapyridoxal 5′-Phosphate Griswold, Wait R.; Toney, Michael D. Journal of the American Chemical Society, Vol. 133, Issue 37 https://doi.org/10.1021/ja2061006	journal	September 2011
NMR Studies of Protonation and Hydrogen Bond States of Internal Aldimines of Pyridoxal 5′-Phosphate Acid–Base in Alanine Racemase, Aspartate Aminotransferase, and Poly- l -lysine Chan-Huot, Monique; Dos, Alexandra; Zander, Reinhard Journal of the American Chemical Society, Vol. 135, Issue 48 https://doi.org/10.1021/ja408988z	journal	November 2013
NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity Caulkins, Bethany G.; Young, Robert P.; Kudla, Ryan A. Journal of the American Chemical Society, Vol. 138, Issue 46 https://doi.org/10.1021/jacs.6b08937	journal	November 2016
¹⁵ N Nuclear Magnetic Resonance Studies of Acid−Base Properties of Pyridoxal-5‘-Phosphate Aldimines in Aqueous Solution Sharif, Shasad; Huot, Monique Chan; Tolstoy, Peter M. The Journal of Physical Chemistry B, Vol. 111, Issue 15 https://doi.org/10.1021/jp067334g	journal	April 2007
DFT Studies on Schiff Base Formation of Vitamin B6 Analogues. Reaction between a Pyridoxamine-Analogue and Carbonyl Compounds Ortega-Castro, J.; Adrover, M.; Frau, J. The Journal of Physical Chemistry A, Vol. 114, Issue 13 https://doi.org/10.1021/jp909156m	journal	April 2010
Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme Dajnowicz, Steven; Johnston, Ryne C.; Parks, Jerry M. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01060-y	journal	October 2017
A genomic overview of pyridoxal-phosphate-dependent enzymes Percudani, Riccardo; Peracchi, Alessio EMBO reports, Vol. 4, Issue 9 https://doi.org/10.1038/sj.embor.embor914	journal	September 2003
Conformation and reaction specificity in pyridoxal phosphate enzymes. Dunathan, H. C. Proceedings of the National Academy of Sciences, Vol. 55, Issue 4 https://doi.org/10.1073/pnas.55.4.712	journal	April 1966
Refinement and Comparisons of the Crystal Structures of Pig Cytosolic Aspartate Aminotransferase and Its Complex with 2-Methylaspartate Rhee, Sangkee; Silva, Mercedes M.; Hyde, C. Craig Journal of Biological Chemistry, Vol. 272, Issue 28 https://doi.org/10.1074/jbc.272.28.17293	journal	July 1997
Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5′-phosphate in aspartate aminotransferase Dajnowicz, Steven; Parks, Jerry M.; Hu, Xiche Journal of Biological Chemistry, Vol. 292, Issue 14 https://doi.org/10.1074/jbc.M116.774588	journal	February 2017
NMR crystallography in the enzyme active site of tryptophan synthase Mueller, Leonard J. Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a1 https://doi.org/10.1107/S0108767317099433	journal	May 2017
Direct observation of protonation states in a PLP-dependent enzyme by neutron crystallography Dajnowicz, Steven; Blakeley, Matthew; Keen, David Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a1 https://doi.org/10.1107/S0108767317099731	journal	May 2017
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Carbon Acidity in Enzyme Active Sites Toney, Michael D. Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00025	journal	February 2019

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Aspartate amino
Dunathan alignment
Hyperconjugation
Low barrier hydrogen bond
Neutron crystallography
PLP fold type I
Pyridoxal 5′-phosphate
Transamination
transferase

Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase

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