1
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Hegazy R, Cristobal JR, Richard JP. Glycerol 3-Phosphate Dehydrogenase Catalyzed Hydride Transfer: Enzyme Activation by Cofactor Pieces. Biochemistry 2024. [PMID: 39319842 DOI: 10.1021/acs.biochem.4c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Glycerol 3-phosphate dehydrogenase catalyzes reversible hydride transfer from glycerol 3-phosphate (G3P) to NAD+ to form dihydroxyacetone phosphate; from the truncated substrate ethylene glycol to NAD+ in a reaction activated by the phosphite dianion substrate fragment; and from G3P to the truncated nicotinamide riboside cofactor in a reaction activated by adenosine 5'-diphosphate, adenosine 5'-monophosphate, and ribose 5-phosphate cofactor fragments. The sum of the stabilization of the transition state for GPDH-catalyzed hydride transfer reactions of the whole substrates by the phosphodianion fragment of G3P and the ADP fragment of NAD+ is 25 kcal/mol. Fourteen kcal/mol of this transition state stabilization is recovered as phosphite dianion and AMP activation of the reactions of the substrate and cofactor fragments. X-ray crystal structures for unliganded GPDH, for a binary GPDH·NAD+ complex, and for a nonproductive ternary GPDH·NAD+·DHAP complex show that the ligand binding energy is utilized to drive an extensive protein conformational change that creates a caged complex for these ligands. The phosphite dianion and AMP fragments are proposed to activate GPDH for the catalysis of hydride transfer by stabilization of this active caged complex. The closure of a conserved loop [292-LNGQKL-297] during substrate binding stabilizes the G3P and NAD+ complexes by interactions, respectively, with the Q295 and K296 loop side chains. The appearance and apparent conservation of two side chains that interact with the hydride donor and acceptor to stabilize the active closed enzyme are proposed to represent a significant improvement in the catalytic performance of GPDH.
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Affiliation(s)
- Rania Hegazy
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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2
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Cristobal J, Hegazy R, Richard JP. Glycerol 3-Phosphate Dehydrogenase: Role of the Protein Conformational Change in Activation of a Readily Reversible Enzyme-Catalyzed Hydride Transfer Reaction. Biochemistry 2024; 63:1016-1025. [PMID: 38546289 PMCID: PMC11025551 DOI: 10.1021/acs.biochem.3c00702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 04/17/2024]
Abstract
Kinetic parameters are reported for glycerol 3-phosphate dehydrogenase (GPDH)-catalyzed hydride transfer from the whole substrate glycerol 3-phosphate (G3P) or truncated substrate ethylene glycol (EtG) to NAD, and for activation of the hydride transfer reaction of EtG by phosphite dianion. These kinetic parameters were combined with parameters for enzyme-catalyzed hydride transfer in the microscopic reverse direction to give the reaction equilibrium constants Keq. Hydride transfer from G3P is favored in comparison to EtG because the carbonyl product of the former reaction is stabilized by hyperconjugative electron donation from the -CH2R keto substituent. The kinetic data show that the phosphite dianion provides the same 7.6 ± 0.1 kcal/mol stabilization of the transition states for enzyme-catalyzed reactions in the forward [reduction of NAD by EtG] and reverse [oxidation of NADH by glycolaldehyde] directions. The experimental evidence that supports a role for phosphite dianion in stabilizing the active closed form of the GPDH (EC) relative to the ca. 6 kcal/mol more unstable open form (EO) is summarized.
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Affiliation(s)
- Judith
R. Cristobal
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Rania Hegazy
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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3
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Hegazy R, Richard JP. Triosephosphate Isomerase: The Crippling Effect of the P168A/I172A Substitution at the Heart of an Enzyme Active Site. Biochemistry 2023; 62:2916-2927. [PMID: 37768194 PMCID: PMC10586322 DOI: 10.1021/acs.biochem.3c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/01/2023] [Indexed: 09/29/2023]
Abstract
The P168 and I172 side chains sit at the heart of the active site of triosephosphate isomerase (TIM) and play important roles in the catalysis of the isomerization reaction. The phosphodianion of substrate glyceraldehyde 3-phosphate (GAP) drives a conformational change at the TIM that creates a steric interaction with the P168 side chain that is relieved by the movement of P168 that carries the basic E167 side chain into a clamp that consists of the hydrophobic I172 and L232 side chains. The P168A/I172A substitution at TIM from Trypanosoma brucei brucei (TbbTIM) causes a large 120,000-fold decrease in kcat for isomerization of GAP that eliminates most of the difference in the reactivity of TIM compared to the small amine base quinuclidinone for deprotonation of catalyst-bound GAP. The I172A substitution causes a > 2-unit decrease in the pKa of the E167 carboxylic acid in a complex to the intermediate analog PGA, but the P168A substitution at the I172A variant has no further effect on this pKa. The P168A/I172A substitutions cause a 5-fold decrease in Km for the isomerization of GAP from a 0.9 kcal/mol stabilization of the substrate Michaelis complexes. The results show that the P168 and I172 side chains play a dual role in destabilizing the ground-state Michaelis complex to GAP and in promoting stabilization of the transition state for substrate isomerization. This is consistent with an important role for these side chains in an induced fit reaction mechanism [Richard, J. P. (2022) Enabling Role of Ligand-Driven Conformational Changes in Enzyme Evolution. Biochemistry 61, 1533-1542].
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Affiliation(s)
- Rania Hegazy
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
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4
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Cristobal J, Nagorski RW, Richard JP. Utilization of Cofactor Binding Energy for Enzyme Catalysis: Formate Dehydrogenase-Catalyzed Reactions of the Whole NAD Cofactor and Cofactor Pieces. Biochemistry 2023; 62:2314-2324. [PMID: 37463347 PMCID: PMC10399567 DOI: 10.1021/acs.biochem.3c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/29/2023] [Indexed: 07/20/2023]
Abstract
The pressure to optimize enzymatic rate accelerations has driven the evolution of the induced-fit mechanism for enzyme catalysts where the binding interactions of nonreacting phosphodianion or adenosyl substrate pieces drive enzyme conformational changes to form protein substrate cages that are activated for catalysis. We report the results of experiments to test the hypothesis that utilization of the binding energy of the adenosine 5'-diphosphate ribose (ADP-ribose) fragment of the NAD cofactor to drive a protein conformational change activates Candida boidinii formate dehydrogenase (CbFDH) for catalysis of hydride transfer from formate to NAD+. The ADP-ribose fragment provides a >14 kcal/mol stabilization of the transition state for CbFDH-catalyzed hydride transfer from formate to NAD+. This is larger than the ca. 6 kcal/mol stabilization of the ground-state Michaelis complex between CbFDH and NAD+ (KNAD = 0.032 mM). The ADP, AMP, and ribose 5'-phosphate fragments of NAD+ activate CbFDH for catalysis of hydride transfer from formate to nicotinamide riboside (NR). At a 1.0 M standard state, these activators stabilize the hydride transfer transition states by ≈5.5 (ADP), 5.5 (AMP), and 4.4 (ribose 5'-phosphate) kcal/mol. We propose that activation by these cofactor fragments is partly or entirely due to the ion-pair interaction between the guanidino side chain cation of R174 and the activator phosphate anion. This substitutes for the interaction between the α-adenosyl pyrophosphate anion of the whole NAD+ cofactor that holds CbFDH in the catalytically active closed conformation.
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Affiliation(s)
- Judith
R. Cristobal
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
| | - Richard W. Nagorski
- Department
of Chemistry, Illinois State University, Normal, Illinois 61790-4160, United
States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United
States
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5
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Cristobal JR, Richard JP. Kinetics and mechanism for enzyme-catalyzed reactions of substrate pieces. Methods Enzymol 2023; 685:95-126. [PMID: 37245916 PMCID: PMC10251411 DOI: 10.1016/bs.mie.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The most important difference between enzyme and small molecule catalysts is that only enzymes utilize the large intrinsic binding energies of nonreacting portions of the substrate in stabilization of the transition state for the catalyzed reaction. A general protocol is described to determine the intrinsic phosphodianion binding energy for enzymatic catalysis of reactions of phosphate monoester substrates, and the intrinsic phosphite dianion binding energy in activation of enzymes for catalysis of phosphodianion truncated substrates, from the kinetic parameters for enzyme-catalyzed reactions of whole and truncated substrates. The enzyme-catalyzed reactions so-far documented that utilize dianion binding interactions for enzyme activation; and, their phosphodianion truncated substrates are summarized. A model for the utilization of dianion binding interactions for enzyme activation is described. The methods for the determination of the kinetic parameters for enzyme-catalyzed reactions of whole and truncated substrates, from initial velocity data, are described and illustrated by graphical plots of kinetic data. The results of studies on the effect of site-directed amino acid substitutions at orotidine 5'-monophosphate decarboxylase, triosephosphate isomerase, and glycerol-3-phosphate dehydrogenase provide strong support for the proposal that these enzymes utilize binding interactions with the substrate phosphodianion to hold the protein catalysts in reactive closed conformations.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY, United States.
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6
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Cristobal JR, Richard JP. Glycerol-3-Phosphate Dehydrogenase: The K120 and K204 Side Chains Define an Oxyanion Hole at the Enzyme Active Site. Biochemistry 2022; 61:856-867. [PMID: 35502876 PMCID: PMC9119304 DOI: 10.1021/acs.biochem.2c00053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cationic K120 and K204 side chains lie close to the C-2 carbonyl group of substrate dihydroxyacetone phosphate (DHAP) at the active site of glycerol-3-phosphate dehydrogenase (GPDH), and the K120 side chain is also positioned to form a hydrogen bond to the C-1 hydroxyl of DHAP. The kinetic parameters for unactivated and phosphite dianion-activated GPDH-catalyzed reduction of glycolaldehyde and acetaldehyde (AcA) show that the transition state for the former reaction is stabilized by ca 5 kcal/mole by interactions of the C-1 hydroxyl group with the protein catalyst. The K120A and K204A substitutions at wild-type GPDH result in similar decreases in kcat, but Km is only affected by the K120A substitution. These results are consistent with 3 kcal/mol stabilizing interactions between the K120 or K204 side chains and a negative charge at the C-2 oxygen at the transition state for hydride transfer from NADH to DHAP. This stabilization resembles that observed at oxyanion holes for other enzymes. There is no detectable rescue of the K204A variant by ethylammonium cation (EtNH3+), compared with the efficient rescue of the K120A variant. This is consistent with a difference in the accessibility of the variant enzyme active sites to exogenous EtNH3+. The K120A/K204A substitutions cause a (6 × 106)-fold increase in the promiscuity of wild-type hlGPDH for catalysis of the reduction of AcA compared to DHAP. This may reflect conservation of the active site for an ancestral alcohol dehydrogenase, whose relative activity for catalysis of reduction of AcA increases with substitutions that reduce the activity for reduction of the specific substrate DHAP.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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7
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Robertson AJ, Cruz-Navarrete FA, Wood HP, Vekaria N, Hounslow AM, Bisson C, Cliff MJ, Baxter NJ, Waltho JP. An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition. ACS Catal 2022; 12:3149-3164. [PMID: 35692864 PMCID: PMC9171722 DOI: 10.1021/acscatal.1c05524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/10/2022] [Indexed: 02/05/2023]
Abstract
Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use β-phosphoglucomutase (βPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. βPGM catalyzes the isomerization of β-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. βPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported β-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.
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Affiliation(s)
- Angus J. Robertson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | | | - Henry P. Wood
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Nikita Vekaria
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrea M. Hounslow
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Claudine Bisson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicola J. Baxter
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
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8
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Pallapati AR, Sirigiri SD, Jain S, Ratnala V, Roy I. Lysine245 plays a crucial role in stability and function of glycerol 3-phosphate dehydrogenase (Gpd1) in Saccharomyces cerevisiae. J Cell Biochem 2021; 122:1726-1736. [PMID: 34369003 DOI: 10.1002/jcb.30125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/10/2021] [Accepted: 07/16/2021] [Indexed: 11/07/2022]
Abstract
Glycerol 3-phosphate dehydrogenase (Gpd1 isoform) catalyzes the rate limiting step of glycerol synthesis and is a critical component of the osmo-responsive machinery in yeast. The three-dimensional structure of the enzyme is similar to the enzyme from many other organisms, including humans. A recent study with the human enzyme has proposed K120 (K152 in yeast) to be in the correct orientation for catalysis; K204 (K245 in yeast) is out of plane and is not a participant in the catalytic cycle. The current work was carried out to establish the role of K245 in the catalytic cycle of yeast Gpd1. K245A mutant was found to possess lower catalytic activity. Osmotically stressed cells expressing Gpd1 (K245A) showed no change in intracellular glycerol as compared with wild-type cells which showed ~60% increase. Fluorescence microscopy, native polyacrylamide gel electrophoresis (PAGE) analysis, fluorescence spectroscopy, and Thioflavin T spectrofluorimetry showed a relatively unstable, aggregation- and degradation-prone conformation for the mutant. In silico studies showed an aggregation "hotspot" around K245. This study establishes the requirement of K245 for conformational stability and functional adaptation of Gpd1 in Saccharomyces cerevisiae.
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Affiliation(s)
- Anusha R Pallapati
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Sri D Sirigiri
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Vamsi Ratnala
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Punjab, India
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9
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Richard JP, Cristobal JR, Amyes TL. Linear Free Energy Relationships for Enzymatic Reactions: Fresh Insight from a Venerable Probe. Acc Chem Res 2021; 54:2532-2542. [PMID: 33939414 PMCID: PMC8157535 DOI: 10.1021/acs.accounts.1c00147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Linear free energy relationships (LFERs) for substituent effects on reactions that
proceed through similar transition states provide insight into transition state
structures. A classical approach to the analysis of LFERs showed that differences in the
slopes of Brønsted correlations for addition of substituted alkyl alcohols to
ring-substituted 1-phenylethyl carbocations and to the β-galactopyranosyl
carbocation intermediate of reactions catalyzed by β-galactosidase provide
evidence that the enzyme catalyst modifies the curvature of the energy surface at the
saddle point for the transition state for nucleophile addition. We have worked to
generalize the use of LFERs in the determination of enzyme mechanisms. The defining
property of enzyme catalysts is their specificity for binding the transition state with
a much higher affinity than the substrate. Triosephosphate isomerase (TIM), orotidine
5′-monophosphate decarboxylase (OMPDC), and glycerol 3-phosphate dehydrogenase
(GPDH) show effective catalysis of reactions of phosphorylated substrates and strong
phosphite dianion activation of reactions of phosphodianion truncated substrates, with
rate constants kcat/Km
(M–1 s–1) and
kcat/KdKHPi
(M–2 s–1), respectively. Good linear logarithmic
correlations, with a slope of 1.1, between these kinetic parameters determined for
reactions catalyzed by five or more variant forms of each catalyst are observed, where
the protein substitutions are mainly at side chains which function to stabilize the cage
complex between the enzyme and substrate. This shows that the enzyme-catalyzed reactions
of a whole substrate and substrate pieces proceed through transition states of similar
structures. It provides support for the proposal that the dianion binding energy of
whole phosphodianion substrates and of phosphite dianion is used to drive the conversion
of these protein catalysts from flexible and entropically rich ground states to stiff
and catalytically active Michaelis complexes that show the same activity toward
catalysis of the reactions of whole and phosphodianion truncated substrates. There is a
good linear correlation, with a slope of 0.73, between values of the dissociation
constants log Ki for release of the transition state analog
phosphoglycolate (PGA) trianion and log
kcat/Km for isomerization of
GAP for wild-type and variants of TIM. This correlation shows that the substituted amino
acid side chains act to stabilize the complex between TIM and the PGA trianion and that
ca. 70% of this stabilization is observed at the transition state for
substrate deprotonation. The correlation provides evidence that these side chains
function to enhance the basicity of the E165 side chain of TIM, which deprotonates the
bound carbon acid substrate. There is a good linear correlation, with a slope of 0.74,
between the values of ΔG‡ and
ΔG° determined by electron valence bond (EVB) calculations
to model deprotonation of dihydroxyacetone phosphate (DHAP) in water and when bound to
wild-type and variant forms of TIM to form the enediolate reaction intermediate. This
correlation provides evidence that the stabilizing interactions of the transition state
for TIM-catalyzed deprotonation of DHAP are optimized by placement of amino acid side
chains in positions that provide for the maximum stabilization of the charged reaction
intermediate, relative to the neutral substrate.
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Affiliation(s)
- John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Judith R. Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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10
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He R, Cristobal JR, Gong NJ, Richard JP. Hydride Transfer Catalyzed by Glycerol Phosphate Dehydrogenase: Recruitment of an Acidic Amino Acid Side Chain to Rescue a Damaged Enzyme. Biochemistry 2020; 59:4856-4863. [PMID: 33305938 PMCID: PMC7784668 DOI: 10.1021/acs.biochem.0c00801] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
K120 of glycerol 3-phosphate dehydrogenase (GPDH) lies close to the carbonyl group of
the bound dihydroxyacetone phosphate (DHAP) dianion. pH rate (pH 4.6–9.0)
profiles are reported for kcat and
(kcat/Km)dianion
for wild type and K120A GPDH-catalyzed reduction of DHAP by NADH, and for
(kcat/KdKam)
for activation of the variant-catalyzed reduction by
CH3CH2NH3+, where
Kam and Kd are apparent
dissociation constants for CH3CH2NH3+ and
DHAP, respectively. These profiles provide evidence that the K120 side chain cation,
which is stabilized by an ion-pairing interaction with the D260 side chain, remains
protonated between pH 4.6 and 9.0. The profiles for wild type and K120A variant GPDH
show downward breaks at a similar pH value (7.6) that are attributed to protonation of
the K204 side chain, which also lies close to the substrate carbonyl oxygen. The pH
profiles for
(kcat/Km)dianion
and
(kcat/KdKam)
for the K120A variant show that the monoprotonated form of the variant is activated for
catalysis by CH3CH2NH3+ but has no
detectable activity, compared to the diprotonated variant, for unactivated reduction of
DHAP. The pH profile for kcat shows that the monoprotonated
K120A variant is active toward reduction of enzyme-bound DHAP, because of activation by
a ligand-driven conformational change. Upward breaks in the pH profiles for
kcat and
(kcat/Km)dianion
for K120A GPDH are attributed to protonation of D260. These breaks are consistent with
the functional replacement of K120 by D260, and a plasticity in the catalytic roles of
the active site side chains.
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Affiliation(s)
- Rui He
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Judith R Cristobal
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - Naiji Jabin Gong
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, The State University of New York at Buffalo, Buffalo, New York 14260-3000, United States
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11
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Yildiz I, Sizirici Yildiz B. Computational mechanistic study of human liver glycerol 3‐phosphate dehydrogenase using ONIOM method. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Mhashal AR, Romero-Rivera A, Mydy LS, Cristobal JR, Gulick AM, Richard JP, Kamerlin SCL. Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. ACS Catal 2020; 10:11253-11267. [PMID: 33042609 PMCID: PMC7536716 DOI: 10.1021/acscatal.0c02757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2020] [Indexed: 11/30/2022]
Abstract
![]()
Glycerol-3-phosphate
dehydrogenase is a biomedically important
enzyme that plays a crucial role in lipid biosynthesis. It is activated
by a ligand-gated conformational change that is necessary for the
enzyme to reach a catalytically competent conformation capable of
efficient transition-state stabilization. While the human form (hlGPDH) has been the subject of extensive structural and
biochemical studies, corresponding computational studies to support
and extend experimental observations have been lacking. We perform
here detailed empirical valence bond and Hamiltonian replica exchange
molecular dynamics simulations of wild-type hlGPDH
and its variants, as well as providing a crystal structure of the
binary hlGPDH·NAD R269A variant where the enzyme
is present in the open conformation. We estimated the activation free
energies for the hydride transfer reaction in wild-type and substituted hlGPDH and investigated the effect of mutations on catalysis
from a detailed structural study. In particular, the K120A and R269A
variants increase both the volume and solvent exposure of the active
site, with concomitant loss of catalytic activity. In addition, the
R269 side chain interacts with both the Q295 side chain on the catalytic
loop, and the substrate phosphodianion. Our structural data and simulations
illustrate the critical role of this side chain in facilitating the
closure of hlGPDH into a catalytically competent
conformation, through modulating the flexibility of a key catalytic
loop (292-LNGQKL-297). This, in turn, rationalizes a tremendous 41,000
fold decrease experimentally in the turnover number, kcat, upon truncating this residue, as loop closure is
essential for both correct positioning of key catalytic residues in
the active site, as well as sequestering the active site from the
solvent. Taken together, our data highlight the importance of this
ligand-gated conformational change in catalysis, a feature that can
be exploited both for protein engineering and for the design of allosteric
inhibitors targeting this biomedically important enzyme.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Adrian Romero-Rivera
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Lisa S. Mydy
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - Judith R. Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Shina C. L. Kamerlin
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
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13
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Pridie C, Ueda K, Simmonds AJ. Rosy Beginnings: Studying Peroxisomes in Drosophila. Front Cell Dev Biol 2020; 8:835. [PMID: 32984330 PMCID: PMC7477296 DOI: 10.3389/fcell.2020.00835] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022] Open
Abstract
Research using the fruit fly Drosophila melanogaster has traditionally focused on understanding how mutations affecting gene regulation or function affect processes linked to animal development. Accordingly, flies have become an essential foundation of modern medical research through repeated contributions to our fundamental understanding of how their homologs of human genes function. Peroxisomes are organelles that metabolize lipids and reactive oxygen species like peroxides. However, despite clear linkage of mutations in human genes affecting peroxisomes to developmental defects, for many years fly models were conspicuously absent from the study of peroxisomes. Now, the few early studies linking the Rosy eye color phenotype to peroxisomes in flies have been joined by a growing body of research establishing novel roles for peroxisomes during the development or function of specific tissues or cell types. Similarly, unique properties of cultured fly Schneider 2 cells have advanced our understanding of how peroxisomes move on the cytoskeleton. Here, we profile how those past and more recent Drosophila studies started to link specific effects of peroxisome dysfunction to organ development and highlight the utility of flies as a model for human peroxisomal diseases. We also identify key differences in the function and proliferation of fly peroxisomes compared to yeast or mammals. Finally, we discuss the future of the fly model system for peroxisome research including new techniques that should support identification of additional tissue specific regulation of and roles for peroxisomes.
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Affiliation(s)
- C Pridie
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Kazuki Ueda
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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14
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Cristobal JR, Reyes AC, Richard JP. The Organization of Active Site Side Chains of Glycerol-3-phosphate Dehydrogenase Promotes Efficient Enzyme Catalysis and Rescue of Variant Enzymes. Biochemistry 2020; 59:1582-1591. [PMID: 32250105 PMCID: PMC7207223 DOI: 10.1021/acs.biochem.0c00175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
A comparison of the
values of kcat/Km for reduction of dihydroxyacetone phosphate
(DHAP) by NADH catalyzed by wild type and K120A/R269A variant glycerol-3-phosphate
dehydrogenase from human liver (hlGPDH) shows that
the transition state for enzyme-catalyzed hydride transfer is stabilized
by 12.0 kcal/mol by interactions with the cationic K120 and R269 side
chains. The transition state for the K120A/R269A variant-catalyzed
reduction of DHAP is stabilized by 1.0 and 3.8 kcal/mol for reactions
in the presence of 1.0 M EtNH3+ and guanidinium
cation (Gua+), respectively, and by 7.5 kcal/mol for reactions
in the presence of a mixture of each cation at 1.0 M, so that the
transition state stabilization by the ternary E·EtNH3+·Gua+ complex is 2.8 kcal/mol greater
than the sum of stabilization by the respective binary complexes.
This shows that there is cooperativity between the paired activators
in transition state stabilization. The effective molarities (EMs)
of ∼50 M determined for the K120A and R269A side chains are
≪106 M, the EM for entropically controlled reactions.
The unusually efficient rescue of the activity of hlGPDH-catalyzed reactions by the HPi/Gua+ pair
and by the Gua+/EtNH3+ activator
pair is due to stabilizing interactions between the protein and the
activator pieces that organize the K120 and R269 side chains at the
active site. This “preorganization” of side chains promotes
effective catalysis by hlGPDH and many other enzymes.
The role of the highly conserved network of side chains, which include
Q295, R269, N270, N205, T264, K204, D260, and K120, in catalysis is
discussed.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Archie C Reyes
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
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15
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The role of ligand-gated conformational changes in enzyme catalysis. Biochem Soc Trans 2020; 47:1449-1460. [PMID: 31657438 PMCID: PMC6824834 DOI: 10.1042/bst20190298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 11/17/2022]
Abstract
Structural and biochemical studies on diverse enzymes have highlighted the importance of ligand-gated conformational changes in enzyme catalysis, where the intrinsic binding energy of the common phosphoryl group of their substrates is used to drive energetically unfavorable conformational changes in catalytic loops, from inactive open to catalytically competent closed conformations. However, computational studies have historically been unable to capture the activating role of these conformational changes. Here, we discuss recent experimental and computational studies, which can remarkably pinpoint the role of ligand-gated conformational changes in enzyme catalysis, even when not modeling the loop dynamics explicitly. Finally, through our joint analyses of these data, we demonstrate how the synergy between theory and experiment is crucial for furthering our understanding of enzyme catalysis.
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16
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Goryanova B, Amyes TL, Richard JP. Role of the Carboxylate in Enzyme-Catalyzed Decarboxylation of Orotidine 5'-Monophosphate: Transition State Stabilization Dominates Over Ground State Destabilization. J Am Chem Soc 2019; 141:13468-13478. [PMID: 31365243 PMCID: PMC6735427 DOI: 10.1021/jacs.9b04823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Kinetic
parameters kex (s–1)
and kex/Kd (M–1 s–1) are reported
for exchange
for deuterium in D2O of the C-6 hydrogen of 5-fluororotidine
5′-monophosphate (FUMP) catalyzed by the Q215A,
Y217F, and Q215A/Y217F variants of yeast orotidine 5′-monophosphate
decarboxylase (ScOMPDC) at pD 8.1, and by the Q215A
variant at pD 7.1–9.3. The pD rate profiles for wildtype ScOMPDC and the Q215A variant are identical, except for
a 2.5 log unit downward displacement in the profile for the Q215A
variant. The Q215A, Y217F and Q215A/Y217F substitutions cause 1.3–2.0
kcal/mol larger increases in the activation barrier for wildtype ScOMPDC-catalyzed deuterium exchange compared with decarboxylation,
because of the stronger apparent side chain interaction with the transition
state for the deuterium exchange reaction. The stabilization of the
transition state for the OMPDC-catalyzed deuterium exchange reaction
of FUMP is ca. 19 kcal/mol smaller than the transition
state for decarboxylation of OMP, and ca. 8 kcal/mol
smaller than for OMPDC-catalyzed deprotonation of FUMP to form the vinyl carbanion intermediate common to OMPDC-catalyzed
reactions OMP/FOMP and UMP/FUMP. We propose
that ScOMPDC shows similar stabilizing interactions
with the common portions of decarboxylation and deprotonation transition
states that lead to formation of this vinyl carbanion intermediate,
and that there is a large ca. (19–8) = 11 kcal/mol stabilization
of the former transition state from interactions with the nascent
CO2 of product. The effects of Q215A and Y217F substitutions
on kcat/Km for decarboxylation of OMP are expressed mainly as
an increase in Km for the reactions catalyzed
by the variant enzymes, while the effects on kex/Kd for deuterium exchange are
expressed mainly as an increase in kex. This shows that the Q215 and Y217 side chains stabilize the Michaelis
complex to OMP for the decarboxylation reaction, compared
with the complex to FUMP for the deuterium exchange reaction.
These results provide strong support for the conclusion that interactions
which stabilize the transition state for ScOMPDC-catalyzed
decarboxylation at a nonpolar enzyme active site dominate over interactions
that destabilize the ground-state Michaelis complex.
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Affiliation(s)
- Bogdana Goryanova
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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17
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Mydy LS, Cristobal JR, Katigbak RD, Bauer P, Reyes AC, Kamerlin SCL, Richard JP, Gulick AM. Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Biochemistry 2019; 58:1061-1073. [PMID: 30640445 DOI: 10.1021/acs.biochem.8b01103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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. 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.
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Affiliation(s)
- Lisa S Mydy
- Department of Structural Biology , University at Buffalo, SUNY , Buffalo , New York 14203 , United States
| | - Judith R Cristobal
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Roberto D Katigbak
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 Uppsala , Sweden
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Andrew M Gulick
- Department of Structural Biology , University at Buffalo, SUNY , Buffalo , New York 14203 , United States
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18
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Reyes AC, Amyes TL, Richard JP. Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase. Biochemistry 2018; 57:4338-4348. [PMID: 29927590 PMCID: PMC6091503 DOI: 10.1021/acs.biochem.8b00536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Large
primary deuterium kinetic isotope effects (1° DKIEs)
on enzyme-catalyzed hydride transfer may be observed when the transferred
hydride tunnels through the energy barrier. The following 1°
DKIEs on kcat/Km and relative reaction driving force are reported for wild-type and
mutant glycerol-3-phosphate dehydrogenase (GPDH)-catalyzed reactions
of NADL (L = H, D): wild-type GPDH, ΔΔG⧧ = 0 kcal/mol, 1° DKIE = 1.5;
N270A, 5.6 kcal/mol, 3.1; R269A, 9.1 kcal/mol, 2.8; R269A + 1.0 M
guanidine, 2.4 kcal/mol, 2.7; R269A/N270A, 11.5 kcal/mol, 2.4. Similar
1° DKIEs were observed on kcat. The
narrow range of 1° DKIEs (2.4–3.1) observed for a 9.1
kcal/mol change in reaction driving force provides strong evidence
that these are intrinsic 1° DKIEs on rate-determining hydride
transfer. Evidence is presented that the intrinsic DKIE on wild-type
GPDH-catalyzed reduction of DHAP lies in this range. A similar range
of 1° DKIEs (2.4–2.9) on (kcat/KGA, M–1 s–1) was reported for dianion-activated hydride transfer from NADL to
glycolaldehyde (GA) [Reyes, A. C.; Amyes, T. L.; Richard, J.
P. J. Am. Chem. Soc.2016, 138, 14526–14529].
These 1° DKIEs are much smaller than those observed for enzyme-catalyzed
hydrogen transfer that occurs mainly by quantum mechanical tunneling.
These results support the conclusion that the rate acceleration for
GPDH-catalyzed reactions is due to the stabilization of the transition
state for hydride transfer by interactions with the protein catalyst.
The small 1° DKIEs reported for mutant GPDH-catalyzed and for
wild-type dianion-activated reactions are inconsistent with a model
where the dianion binding energy is utilized in the stabilization
of a tunneling ready state.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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19
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Reyes AC, Amyes TL, Richard JP. A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer. Org Biomol Chem 2018; 15:8856-8866. [PMID: 28956050 DOI: 10.1039/c7ob01652b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
There is no consensus of opinion on the origin of the large rate accelerations observed for enzyme-catalyzed hydride transfer. The interpretation of recent results from studies on hydride transfer reactions catalyzed by alcohol dehydrogenase (ADH) focus on the proposal that the effective barrier height is reduced by quantum-mechanical tunneling through the energy barrier. This interpretation contrasts sharply with the notion that enzymatic rate accelerations are obtained through direct stabilization of the transition state for the nonenzymatic reaction in water. The binding energy of the dianion of substrate DHAP provides 11 kcal mol-1 stabilization of the transition state for the hydride transfer reaction catalyzed by glycerol-3-phosphate dehydrogenase (GPDH). We summarize evidence that the binding interactions between (GPDH) and dianion activators are utilized directly for stabilization of the transition state for enzyme-catalyzed hydride transfer. The possibility is considered, and then discounted, that these dianion binding interactions are utilized for the stabilization of a tunnel ready state (TRS) that enables efficient tunneling of the transferred hydride through the energy barrier, and underneath the energy maximum for the transition state. It is noted that the evidence to support the existence of a tunnel-ready state for the hydride transfer reactions catalyzed by ADH is ambiguous. We propose that the rate acceleration for ADH is due to the utilization of the binding energy of the cofactor NAD+/NADH in the stabilization of the transition state for enzyme-catalyzed hydride transfer.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA.
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20
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He R, Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: The Role of a Flexible Loop in Activation of Glycerol-3-phosphate Dehydrogenase for Catalysis of Hydride Transfer. Biochemistry 2018; 57:3227-3236. [PMID: 29337541 PMCID: PMC6001809 DOI: 10.1021/acs.biochem.7b01282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The side chain of Q295 of glycerol-3-phosphate
dehydrogenase from
human liver (hlGPDH) lies in a flexible loop, that
folds over the phosphodianion of substrate dihydroxyacetone phosphate
(DHAP). Q295 interacts with the side-chain cation from R269, which
is ion-paired to the substrate phosphodianion. Kinetic parameters kcat/Km (M–1 s–1) and kcat/KGAKHPi (M–2 s–1) were determined, respectively, for catalysis
of the reduction of DHAP and for dianion activation of catalysis of
reduction of glycolaldehyde (GA) catalyzed by wild-type, Q295G, Q295S,
Q295A, and Q295N mutants of hlGPDH. These mutations
result in up to a 150-fold decrease in (kcat/Km)DHAP and up to a 2.7 kcal/mol
decrease in the intrinsic phosphodianion binding energy. The data
define a linear correlation with slope 1.1, between the intrinsic
phosphodianion binding energy and the intrinsic phosphite dianion
binding energy for activation of hlGPDH-catalyzed
reduction of GA, that demonstrates a role for Q295 in optimizing this
dianion binding energy. The R269A mutation of wild-type GPDH results
in a 9.1 kcal/mol destabilization of the transition state for reduction
of DHAP, but the same R269A mutation of N270A and Q295A mutants result
in smaller 5.9 and 4.9 kcal/mol transition-state destabilization.
Similarly, the N270A or Q295A mutations of R269A GPDH each result
in large falloffs in the efficiency of rescue of the R269A mutant
by guanidine cation. We conclude that N270, which interacts for the
substrate phosphodianion and Q295, which interacts with the guanidine
side chain of R269, function to optimize the apparent
transition-state stabilization provided by the cationic side chain
of R269.
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Affiliation(s)
- Rui He
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Archie C Reyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - Tina L Amyes
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
| | - John P Richard
- Department of Chemistry , University at Buffalo, SUNY , Buffalo , New York 14260-3000 , United States
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21
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Chang HC, Kung CCH, Chang TT, Jao SC, Hsu YT, Li WS. Investigation of the proton relay system operative in human cystosolic aminopeptidase P. PLoS One 2018; 13:e0190816. [PMID: 29351301 PMCID: PMC5774706 DOI: 10.1371/journal.pone.0190816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/20/2017] [Indexed: 11/19/2022] Open
Abstract
Aminopeptidase P, a metalloprotease, targets Xaa-Proline peptides for cleavage [1-4]. There are two forms of human AMPP, a membrane-bound form (hmAMPP) and a soluble cytosolic form (hcAMPP)[5]. Similar to the angiotensin-I-converting enzyme, AMPP plays an important role in the catabolism of inflammatory and vasoactive peptides, known as kinins. The plasma kinin, bradykinin, was used as the substrate to conduct enzymatic activity analyses and to determine the Michaelis constant (Km) of 174 μM and the catalytic rate constant (kcat) of 10.8 s-1 for hcAMPP. Significant differences were observed in the activities of Y527F and R535A hcAMPP mutants, which displayed a 6-fold and 13.5-fold for decrease in turnover rate, respectively. Guanidine hydrochloride restored the activity of R535A hcAMPP, increasing the kcat/Km 20-fold, yet it had no impact on the activities of the wild-type or Y527F mutant hcAMPPs. Activity restoration by guanidine derivatives followed the order guanidine hydrochloride >> methyl-guanidine > amino-guanidine > N-ethyl-guanidine. Overall, the results indicate the participation of R535 in the hydrogen bond network that forms a proton relay system. The quaternary structure of hcAMPP was determined by using analytical ultracentrifugation (AUC). The results show that alanine replacement of Arg535 destabilizes the hcAMPP dimer and that guanidine hydrochloride restores the native monomer-dimer equilibrium. It is proposed that Arg535 plays an important role in hcAMMP catalysis and in stabilization of the catalytically active dimeric state.
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Affiliation(s)
| | | | | | - Shu-Chuan Jao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Hsu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Shan Li
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
- * E-mail:
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22
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Amyes TL, Malabanan MM, Zhai X, Reyes AC, Richard JP. Enzyme activation through the utilization of intrinsic dianion binding energy. Protein Eng Des Sel 2017; 30:157-165. [PMID: 27903763 DOI: 10.1093/protein/gzw064] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022] Open
Abstract
43 We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed.
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Affiliation(s)
- T L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - M M Malabanan
- Department of Biochemistry, Vanderbilt University, Nashville, TN37205-0146, USA
| | - X Zhai
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843-2128, USA
| | - A C Reyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - J P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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23
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Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: Self-Assembly of Enzyme and Substrate Pieces of Glycerol-3-Phosphate Dehydrogenase into a Robust Catalyst of Hydride Transfer. J Am Chem Soc 2016; 138:15251-15259. [PMID: 27792325 PMCID: PMC5291162 DOI: 10.1021/jacs.6b09936] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The stabilization of the transition
state for hlGPDH-catalyzed reduction of DHAP due
to the action of the phosphodianion
of DHAP and the cationic side chain of R269 is between 12.4 and 17
kcal/mol. The R269A mutation of glycerol-3-phosphate dehydrogenase
(hlGPDH) results in a 9.1 kcal/mol destabilization
of the transition state for enzyme-catalyzed reduction of dihydroxyacetone
phosphate (DHAP) by NADH, and there is a 6.7 kcal/mol stabilization of this transition state by 1.0 M guanidine cation (Gua+) [J. Am. Chem. Soc.2015, 137, 5312–5315]. The R269A mutant shows no detectable
activity toward reduction of glycolaldehyde (GA), or activation of
this reaction by 30 mM HPO32–. We report
the unprecedented self-assembly of R269A hlGPDH,
dianions (X2– = FPO32–, HPO32–, or SO42–), Gua+ and GA into a functioning catalyst of the reduction
of GA, and fourth-order reaction rate constants kcat/KGAKXKGua. The linear logarithmic correlation
(slope = 1.0) between values of kcat/KGAKX for dianion
activation of wildtype hlGPDH-catalyzed reduction
of GA and kcat/KGAKXKGua shows that the electrostatic interaction between exogenous dianions
and the side chain of R269 is not significantly perturbed by cutting hlGPDH into R269A and Gua+ pieces. The advantage
for connection of hlGPDH (R269A mutant + Gua+) and substrate pieces (GA + HPi) pieces, (ΔGS‡)HPi+E+Gua = 5.6 kcal/mol, is nearly equal to the sum
of the advantage to connection of the substrate pieces, (ΔGS‡)GA+HPi = 3.3 kcal/mol, for wildtype hlGPDH-catalyzed reaction of GA + HPi, and for connection
of the enzyme pieces, (ΔGS‡)E+Gua = 2.4
kcal/mol, for Gua+ activation of the R269A hlGPDH-catalyzed reaction of DHAP.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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Reyes AC, Amyes TL, Richard JP. Structure-Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. J Am Chem Soc 2016; 138:14526-14529. [PMID: 27769116 PMCID: PMC5105681 DOI: 10.1021/jacs.6b07028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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Primary deuterium
kinetic isotope effects (1°DKIE) on (kcat/KGA, M–1 s–1) for dianion (X2–) activated
hydride transfer from NADL to glycolaldehyde (GA) catalyzed by glycerol-3-phosphate
dehydrogenase were determined over a 2100-fold range of enzyme reactivity:
(X2–, 1°DKIE); FPO32–, 2.8 ± 0.1; HPO32–, 2.5 ±
0.1; SO42–, 2.8 ± 0.2; HOPO32–, 2.5 ± 0.1; S2O32–, 2.9 ± 0.1; unactivated; 2.4 ± 0.2.
Similar 1°DKIEs were determined for kcat. The observed 1°DKIEs are essentially independent of changes
in enzyme reactivity with changing dianion activator. The results
are consistent with (i) fast and reversible ligand binding; (ii) the
conclusion that the observed 1°DKIEs are equal to the intrinsic
1°DKIE on hydride transfer from NADL to GA; (iii) similar intrinsic
1°DKIEs on GPDH-catalyzed reduction of the substrate pieces and
the whole physiological substrate dihydroxyacetone phosphate. The
ground-state binding interactions for different X2– are similar, but there are large differences in the transition state
interactions for different X2–. The changes in transition
state binding interactions are expressed as changes in kcat and are proposed to represent changes in stabilization
of the active closed form of GPDH. The 1°DKIEs are much smaller
than observed for enzyme-catalyzed hydrogen transfer that occurs mainly
by quantum-mechanical tunneling.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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25
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Arcus VL, Prentice EJ, Hobbs JK, Mulholland AJ, Van der Kamp MW, Pudney CR, Parker EJ, Schipper LA. On the Temperature Dependence of Enzyme-Catalyzed Rates. Biochemistry 2016; 55:1681-8. [DOI: 10.1021/acs.biochem.5b01094] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Vickery L. Arcus
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Erica J. Prentice
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Joanne K. Hobbs
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
| | | | | | - Christopher R. Pudney
- Department
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Emily J. Parker
- Biomolecular
Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand
| | - Louis A. Schipper
- School
of Science, University of Waikato, Hamilton 3240, New Zealand
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26
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Reyes AC, Amyes TL, Richard JP. Enzyme Architecture: A Startling Role for Asn270 in Glycerol 3-Phosphate Dehydrogenase-Catalyzed Hydride Transfer. Biochemistry 2016; 55:1429-32. [PMID: 26926520 PMCID: PMC4812618 DOI: 10.1021/acs.biochem.6b00116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The
side chains of R269 and N270 interact with the phosphodianion
of dihydroxyacetone phosphate (DHAP) bound to glycerol 3-phosphate
dehydrogenase (GPDH). The R269A, N270A, and R269A/N270A mutations
of GPDH result in 9.1, 5.6, and 11.5 kcal/mol destabilization, respectively,
of the transition state for GPDH-catalyzed reduction of DHAP by the
reduced form of nicotinamide adenine dinucleotide. The N270A mutation
results in a 7.7 kcal/mol decrease in the intrinsic phosphodianion
binding energy, which is larger than the 5.6 kcal/mol effect of the
mutation on the stability of the transition state for reduction of
DHAP; a 2.2 kcal/mol stabilization of the transition state for unactivated
hydride transfer to the truncated substrate glycolaldehyde (GA); and
a change in the effect of phosphite dianion on GPDH-catalyzed reduction
of GA, from strongly activating to inhibiting. The N270A mutation
breaks the network of hydrogen bonding side chains, Asn270, Thr264,
Asn205, Lys204, Asp260, and Lys120, which connect the dianion activation
and catalytic sites of GPDH. We propose that this disruption dramatically
alters the performance of GPDH at these sites.
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Affiliation(s)
- Archie C Reyes
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260-3000, United States
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27
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Xu XY, Chen QC, Yu YD, Huang XC. Ligand Induced Anionic Cuprous Cyanide Framework for Cupric Ion Turn on Luminescence Sensing and Photocatalytic Degradation of Organic Dyes. Inorg Chem 2015; 55:75-82. [DOI: 10.1021/acs.inorgchem.5b01820] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xiao-Yan Xu
- Department
of Chemistry and Key Laboratory for Preparation and Application of
Ordered Structural Materials of Guangdong Province, Shantou University, Shantou 515063, China
| | - Qiu-Cheng Chen
- Department
of Chemistry and Key Laboratory for Preparation and Application of
Ordered Structural Materials of Guangdong Province, Shantou University, Shantou 515063, China
| | - Ya-Dong Yu
- Department
of Chemistry and Key Laboratory for Preparation and Application of
Ordered Structural Materials of Guangdong Province, Shantou University, Shantou 515063, China
| | - Xiao-Chun Huang
- Department
of Chemistry and Key Laboratory for Preparation and Application of
Ordered Structural Materials of Guangdong Province, Shantou University, Shantou 515063, China
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28
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Zhai X, Amyes TL, Richard JP. Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase. J Am Chem Soc 2015; 137:15185-97. [PMID: 26570983 PMCID: PMC4694050 DOI: 10.1021/jacs.5b09328] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The side chains of
Y208 and S211 from loop 7 of triosephosphate
isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls
from loop 6 to stabilize the caged enzyme–substrate complex.
The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G,
S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions
of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde
3-phosphate [(kcat/Km)GAP and (kcat/Km)DHAP] and of the substrate pieces
glycolaldehyde and phosphite dianion (kcat/KHPiKGA)
are reported. The linear logarithmic correlation between these kinetic
parameters, with slope of 1.04 ± 0.03, shows that most mutations
of TIM result in an identical change in the activation barriers for
the catalyzed reactions of whole substrate and substrate pieces, so
that the transition states for these reactions are stabilized by similar
interactions with the protein catalyst. The second linear logarithmic
correlation [slope = 0.53 ± 0.16] between kcat for isomerization of GAP and Kd⧧ for phosphite dianion binding to the transition
state for wildtype and many mutant TIM-catalyzed reactions of substrate
pieces shows that ca. 50% of the wildtype TIM dianion binding energy,
eliminated by these mutations, is expressed at the wildtype Michaelis
complex, and ca. 50% is only expressed at the wildtype transition
state. Negative deviations from this correlation are observed when
the mutation results in a decrease in enzyme reactivity at the catalytic
site. The main effect of Y208T, Y208S, and Y208A mutations is to cause
a reduction in the total intrinsic dianion binding energy, but the
effect of Y208F extends to the catalytic site.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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29
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Goryanova B, Goldman L, Ming S, Amyes TL, Gerlt JA, Richard JP. Rate and Equilibrium Constants for an Enzyme Conformational Change during Catalysis by Orotidine 5'-Monophosphate Decarboxylase. Biochemistry 2015; 54:4555-64. [PMID: 26135041 PMCID: PMC4520626 DOI: 10.1021/acs.biochem.5b00591] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/01/2015] [Indexed: 11/29/2022]
Abstract
The caged complex between orotidine 5'-monophosphate decarboxylase (ScOMPDC) and 5-fluoroorotidine 5'-monophosphate (FOMP) undergoes decarboxylation ∼300 times faster than the caged complex between ScOMPDC and the physiological substrate, orotidine 5'-monophosphate (OMP). Consequently, the enzyme conformational changes required to lock FOMP at a protein cage and release product 5-fluorouridine 5'-monophosphate (FUMP) are kinetically significant steps. The caged form of ScOMPDC is stabilized by interactions between the side chains from Gln215, Tyr217, and Arg235 and the substrate phosphodianion. The control of these interactions over the barrier to the binding of FOMP and the release of FUMP was probed by determining the effect of all combinations of single, double, and triple Q215A, Y217F, and R235A mutations on kcat/Km and kcat for turnover of FOMP by wild-type ScOMPDC; its values are limited by the rates of substrate binding and product release, respectively. The Q215A and Y217F mutations each result in an increase in kcat and a decrease in kcat/Km, due to a weakening of the protein-phosphodianion interactions that favor fast product release and slow substrate binding. The Q215A/R235A mutation causes a large decrease in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of OMP, which are limited by the rate of the decarboxylation step, but much smaller decreases in the kinetic parameters for ScOMPDC-catalyzed decarboxylation of FOMP, which are limited by the rate of enzyme conformational changes. By contrast, the Y217A mutation results in large decreases in kcat/Km for ScOMPDC-catalyzed decarboxylation of both OMP and FOMP, because of the comparable effects of this mutation on rate-determining decarboxylation of enzyme-bound OMP and on the rate-determining enzyme conformational change for decarboxylation of FOMP. We propose that kcat = 8.2 s(-1) for decarboxylation of FOMP by the Y217A mutant is equal to the rate constant for cage formation from the complex between FOMP and the open enzyme, that the tyrosyl phenol group stabilizes the closed form of ScOMPDC by hydrogen bonding to the substrate phosphodianion, and that the phenyl group of Y217 and F217 facilitates formation of the transition state for the rate-limiting conformational change. An analysis of kinetic data for mutant enzyme-catalyzed decarboxylation of OMP and FOMP provides estimates for the rate and equilibrium constants for the conformational change that traps FOMP at the enzyme active site.
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Affiliation(s)
- Bogdana Goryanova
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Lawrence
M. Goldman
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Shonoi Ming
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - John A. Gerlt
- Departments
of Biochemistry and Chemistry, University
of Illinois, Urbana, Illinois 61801, United
States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
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