Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies

Mydy, Lisa S.; Cristobal, Judith R.; Katigbak, Roberto D.; Bauer, Paul; Reyes, Archie C.; Kamerlin, Shina Caroline Lynn; Richard, John P.; Gulick, Andrew M.

doi:10.1021/acs.biochem.8b01103

Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies

Journal Article · Mon Jan 14 00:00:00 EST 2019 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.8b01103· OSTI ID:1497171

Mydy, Lisa S. ^[1]; Cristobal, Judith R. ^[1]; Katigbak, Roberto D. ^[1]; Bauer, Paul ^[2]; ^[1]; ^[2]; ^[1]; ^[1]

Univ. at Buffalo, SUNY, Buffalo, NY (United States)
Uppsala Univ. (Sweden)

Human liver glycerol 3-phosphate dehydrogenase (hlGPDH) catalyzes the reduction of dihydroxyacetone phosphate (DHAP) to form glycerol 3-phosphate, using the binding energy associated with the nonreacting phosphodianion of the substrate to properly orient the enzyme–substrate complex within the active site. Herein, we report the crystal structures for unliganded, binary E·NAD, and ternary E·NAD·DHAP complexes of wild type hlGPDH, illustrating a new position of DHAP, and probe the kinetics of multiple mutant enzymes with natural and truncated substrates. Mutation of Lys120, which is positioned to donate a proton to the carbonyl of DHAP, results in similar increases in the activation barrier to hlGPDH-catlyzed reduction of DHAP and to phosphite dianion-activated reduction of glycolaldehyde, illustrating that these transition states show similar interactions with the cationic K120 side chain. The K120A mutation results in a 5.3 kcal/mol transition state destabilization, and 3.0 kcal/mol of the lost transition state stabilization is rescued by 1.0 M ethylammonium cation. The 6.5 kcal/mol increase in the activation barrier observed for the D260G mutant hlGPDH-catalyzed reaction represents a 3.5 kcal/mol weakening of transition state stabilization by the K120A side chain and a 3.0 kcal/mol weakening of the interactions with other residues. The interactions, at the enzyme active site, between the K120 side chain and the Q295 and R269 side chains were likewise examined by double-mutant analyses. Here, these results provide strong evidence that the enzyme rate acceleration is due mainly or exclusively to transition state stabilization by electrostatic interactions with polar amino acid side chains.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Cancer Inst.; National Inst. of General Medical Sciences; National Inst. of Health; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1497171

Journal Information:: Biochemistry, Journal Name: Biochemistry Journal Issue: 8 Vol. 58; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (50)

Enzyme Architecture: A Startling Role for Asn270 in Glycerol 3-Phosphate Dehydrogenase-Catalyzed Hydride Transfer Reyes, Archie C.; Amyes, Tina L.; Richard, John P. Biochemistry, Vol. 55, Issue 10 https://doi.org/10.1021/acs.biochem.6b00116	journal	March 2016
Enzyme Architecture: The Role of a Flexible Loop in Activation of Glycerol-3-phosphate Dehydrogenase for Catalysis of Hydride Transfer He, Rui; Reyes, Archie C.; Amyes, Tina L. Biochemistry, Vol. 57, Issue 23 https://doi.org/10.1021/acs.biochem.7b01282	journal	January 2018
Enzymatic Catalysis of Proton Transfer at Carbon: Activation of Triosephosphate Isomerase by Phosphite Dianion Amyes, Tina L.; Richard, John P. Biochemistry, Vol. 46, Issue 19 https://doi.org/10.1021/bi700409b	journal	April 2007
Enzyme Architecture: Deconstruction of the Enzyme-Activating Phosphodianion Interactions of Orotidine 5′-Monophosphate Decarboxylase Goldman, Lawrence M.; Amyes, Tina L.; Goryanova, Bogdana Journal of the American Chemical Society, Vol. 136, Issue 28 https://doi.org/10.1021/ja505037v	journal	July 2014
The Activating Oxydianion Binding Domain for Enzyme-Catalyzed Proton Transfer, Hydride Transfer, and Decarboxylation: Specificity and Enzyme Architecture Reyes, Archie C.; Zhai, Xiang; Morgan, Kelsey T. Journal of the American Chemical Society, Vol. 137, Issue 3 https://doi.org/10.1021/ja5123842	journal	January 2015
Enzyme Architecture: Optimization of Transition State Stabilization from a Cation–Phosphodianion Pair Reyes, Archie C.; Koudelka, Astrid P.; Amyes, Tina L. Journal of the American Chemical Society, Vol. 137, Issue 16 https://doi.org/10.1021/jacs.5b02202	journal	April 2015
Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase Zhai, Xiang; Amyes, Tina L.; Richard, John P. Journal of the American Chemical Society, Vol. 137, Issue 48 https://doi.org/10.1021/jacs.5b09328	journal	November 2015
Enzyme Architecture: Self-Assembly of Enzyme and Substrate Pieces of Glycerol-3-Phosphate Dehydrogenase into a Robust Catalyst of Hydride Transfer Reyes, Archie C.; Amyes, Tina L.; Richard, John P. Journal of the American Chemical Society, Vol. 138, Issue 46 https://doi.org/10.1021/jacs.6b09936	journal	November 2016
Dihydroxyacetone phosphate. Its structure and reactivity with α-glycerophosphate dehydrogenase, aldolase and triose phosphate isomerase and some possible metabolic implications Reynolds, S. J.; Yates, D. W.; Pogson, C. I. Biochemical Journal, Vol. 122, Issue 3 https://doi.org/10.1042/bj1220285	journal	April 1971
Purification and properties of rabbit muscle l-glycerol 3-phosphate dehydrogenase Bentley, Philip; Dickinson, F. Mark; Jones, Ian G. Biochemical Journal, Vol. 135, Issue 4 https://doi.org/10.1042/bj1350853	journal	December 1973
The Kinetics and Mechanism of Action of Rabbit Muscle l-α-Glycerol Phosphate Dehydrogenase Bentley, Philip; Dickinson, F. Mark Biochemical Society Transactions, Vol. 1, Issue 3 https://doi.org/10.1042/bst0010663	journal	May 1973
Application of a Theory of Enzyme Specificity to Protein Synthesis Koshland, D. E. Proceedings of the National Academy of Sciences, Vol. 44, Issue 2 https://doi.org/10.1073/pnas.44.2.98	journal	February 1958
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/s0907444910048675	journal	March 2011
Human glucose-6-phosphate dehydrogenase Lysine 205 is dispensable for substrate binding but essential for catalysis Bautista, JoséM.; Mason, Philip J.; Luzzatto, Lucio FEBS Letters, Vol. 366, Issue 1 https://doi.org/10.1016/0014-5793(95)00474-N	journal	June 1995
Leishmania mexicana Glycerol-3-phosphate Dehydrogenase Showed Conformational Changes Upon Binding a Bi-substrate Adduct Choe, Jungwoo; Guerra, Daniel; Michels, Paul A. M. Journal of Molecular Biology, Vol. 329, Issue 2 https://doi.org/10.1016/S0022-2836(03)00421-2	journal	May 2003
A deliberate approach to screening for initial crystallization conditions of biological macromolecules Luft, Joseph R.; Collins, Robert J.; Fehrman, Nancy A. Journal of Structural Biology, Vol. 142, Issue 1 https://doi.org/10.1016/S1047-8477(03)00048-0	journal	April 2003
Conformational changes and catalysis by alcohol dehydrogenase Plapp, Bryce V. Archives of Biochemistry and Biophysics, Vol. 493, Issue 1 https://doi.org/10.1016/j.abb.2009.07.001	journal	January 2010
Modeling electrostatic effects in proteins Warshel, Arieh; Sharma, Pankaz K.; Kato, Mitsunori Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1764, Issue 11 https://doi.org/10.1016/j.bbapap.2006.08.007	journal	November 2006
Enzyme architecture: on the importance of being in a protein cage Richard, John P.; Amyes, Tina L.; Goryanova, Bogdana Current Opinion in Chemical Biology, Vol. 21 https://doi.org/10.1016/j.cbpa.2014.03.001	journal	August 2014
Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1) Ou, Xianjin; Ji, Chaoneng; Han, Xueqing Journal of Molecular Biology, Vol. 357, Issue 3 https://doi.org/10.1016/j.jmb.2005.12.074	journal	March 2006
A role for flexible loops in enzyme catalysis Malabanan, M. Merced; Amyes, Tina L.; Richard, John P. Current Opinion in Structural Biology, Vol. 20, Issue 6 https://doi.org/10.1016/j.sbi.2010.09.005	journal	December 2010
Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase Reyes, Archie C.; Amyes, Tina L.; Richard, John P. Biochemistry, Vol. 57, Issue 29 https://doi.org/10.1021/acs.biochem.8b00536	journal	June 2018
Phosphate Binding Energy and Catalysis by Small and Large Molecules Morrow, Janet R.; Amyes, Tina L.; Richard, John P. Accounts of Chemical Research, Vol. 41, Issue 4 https://doi.org/10.1021/ar7002013	journal	February 2008
Role of Lys-12 in Catalysis by Triosephosphate Isomerase: A Two-Part Substrate Approach Go, Maybelle K.; Koudelka, Astrid; Amyes, Tina L. Biochemistry, Vol. 49, Issue 25 https://doi.org/10.1021/bi100538b	journal	June 2010
Mutant IDH1 Enhances the Production of 2-Hydroxyglutarate Due to Its Kinetic Mechanism Rendina, Alan R.; Pietrak, Beth; Smallwood, Angela Biochemistry, Vol. 52, Issue 26 https://doi.org/10.1021/bi400514k	journal	June 2013
A Substrate in Pieces: Allosteric Activation of Glycerol 3-Phosphate Dehydrogenase (NAD ⁺ ) by Phosphite Dianion Tsang, Wing-Yin; Amyes, Tina L.; Richard, John P. Biochemistry, Vol. 47, Issue 16 https://doi.org/10.1021/bi8001743	journal	April 2008
A Lysine-Tyrosine Pair Carries Out Acid−Base Chemistry in the Metal Ion-Dependent Pyridine Dinucleotide-Linked β-Hydroxyacid Oxidative Decarboxylases ^† Aktas, Deniz F.; Cook, Paul F. Biochemistry, Vol. 48, Issue 16 https://doi.org/10.1021/bi8022976	journal	April 2009
Structure−Reactivity Relationships for β-Galactosidase (Escherichia coli, lac Z). 4. Mechanism for Reaction of Nucleophiles with the Galactosyl-Enzyme Intermediates of E461G and E461Q β-Galactosidases Richard, John P.; Huber, Reuben E.; Heo, Christine Biochemistry, Vol. 35, Issue 38 https://doi.org/10.1021/bi961029b	journal	January 1996
Gas-phase acidities of amines Brauman, John I.; Blair, Larry K. Journal of the American Chemical Society, Vol. 93, Issue 16 https://doi.org/10.1021/ja00745a015	journal	August 1971
Competitive Inhibition by Substrate during Enzyme Action. Evidence for the Induced-fit Theory^1,2 Thoma, John A.; Koshland, D. E. Journal of the American Chemical Society, Vol. 82, Issue 13 https://doi.org/10.1021/ja01498a025	journal	July 1960
Reduction of an Aldehyde by a NADH/Zn²⁺-Dependent Redox Active Ribozyme Tsukiji, Shinya; Pattnaik, Swetansu B.; Suga, Hiroaki Journal of the American Chemical Society, Vol. 126, Issue 16 https://doi.org/10.1021/ja0495213	journal	April 2004
Activation of Orotidine 5‘-Monophosphate Decarboxylase by Phosphite Dianion: The Whole Substrate is the Sum of Two Parts Amyes, Tina L.; Richard, John P.; Tait, James J. Journal of the American Chemical Society, Vol. 127, Issue 45 https://doi.org/10.1021/ja055493s	journal	October 2005
Enzyme Architecture: Remarkably Similar Transition States for Triosephosphate Isomerase-Catalyzed Reactions of the Whole Substrate and the Substrate in Pieces Zhai, Xiang; Amyes, Tina L.; Richard, John P. Journal of the American Chemical Society, Vol. 136, Issue 11 https://doi.org/10.1021/ja501103b	journal	March 2014
Structure–Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase Reyes, Archie C.; Amyes, Tina L.; Richard, John P. Journal of the American Chemical Society, Vol. 138, Issue 44 https://doi.org/10.1021/jacs.6b07028	journal	October 2016
Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator Hwang, Sunhee; Mruk, Karen; Rahighi, Simin Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06447-z	journal	October 2018
A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer Reyes, Archie C.; Amyes, Tina L.; Richard, John P. Organic & Biomolecular Chemistry, Vol. 15, Issue 42 https://doi.org/10.1039/C7OB01652B	journal	January 2017
A study of the coenzyme-binding characteristics of rabbit muscle l-glycerol 3-phosphate dehydrogenase Bentley, Philip; Dickinson, F. Mark Biochemical Journal, Vol. 143, Issue 1 https://doi.org/10.1042/bj1430011	journal	October 1974
Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites Warshel, Arieh Journal of Biological Chemistry, Vol. 273, Issue 42 https://doi.org/10.1074/jbc.273.42.27035	journal	October 1998
Structure and Mechanism of Human UDP-glucose 6-Dehydrogenase Egger, Sigrid; Chaikuad, Apirat; Kavanagh, Kathryn L. Journal of Biological Chemistry, Vol. 286, Issue 27 https://doi.org/10.1074/jbc.M111.234682	journal	April 2011
Structural and Kinetic Evidence That Catalytic Reaction of Human UDP-glucose 6-Dehydrogenase Involves Covalent Thiohemiacetal and Thioester Enzyme Intermediates Egger, Sigrid; Chaikuad, Apirat; Klimacek, Mario Journal of Biological Chemistry, Vol. 287, Issue 3 https://doi.org/10.1074/jbc.M111.313015	journal	January 2012
Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase McFarlane, Jeffrey S.; Davis, Cara L.; Lamb, Audrey L. Journal of Biological Chemistry, Vol. 293, Issue 21 https://doi.org/10.1074/jbc.RA118.002007	journal	May 2018
The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins Girdlestone, Christopher; Hayward, Steven Journal of Computational Biology, Vol. 23, Issue 1 https://doi.org/10.1089/cmb.2015.0143	journal	January 2016
Pentaerythritol propoxylate: a new crystallization agent and cryoprotectant induces crystal growth of 2-methylcitrate dehydratase Gulick, Andrew M.; Horswill, Alexander R.; Thoden, James B. Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 2 https://doi.org/10.1107/S0907444901018832	journal	January 2002
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
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
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910048675	journal	March 2011
Structures of lactate dehydrogenase A (LDHA) in apo, ternary and inhibitor-bound forms Kolappan, Subramaniapillai; Shen, David L.; Mosi, Renee Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 2 https://doi.org/10.1107/S1399004714024791	journal	January 2015
Three-dimensional structures of the three human class I alcohol dehydrogenases Niederhut, M. S. Protein Science, Vol. 10, Issue 4 https://doi.org/10.1110/ps.45001	journal	April 2001
KINETIC STUDIES ON THE MECHANISM OF CYTOPLASMIC L-α-GLYCEROPHOSPHATE DEHYDROGENASE OF RABBIT SKELETAL MUSCLE Black, William J. Canadian Journal of Biochemistry, Vol. 44, Issue 10 https://doi.org/10.1139/o66-150	journal	October 1966

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