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Chen Z, Li J, Meng L, Li J, Hao Y, Jiang T, Yang X, Li Y, Liu ZP, Gong M. Ligand vacancy channels in pillared inorganic-organic hybrids for electrocatalytic organic oxidation with enzyme-like activities. Nat Commun 2023; 14:1184. [PMID: 36864050 PMCID: PMC9981682 DOI: 10.1038/s41467-023-36830-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/14/2023] [Indexed: 03/04/2023] Open
Abstract
Simultaneously achieving abundant and well-defined active sites with high selectivity has been one of the ultimate goals for heterogeneous catalysis. Herein, we construct a class of Ni hydroxychloride-based inorganic-organic hybrid electrocatalysts with the inorganic Ni hydroxychloride chains pillared by the bidentate N-N ligands. The precise evacuation of N-N ligands under ultrahigh-vacuum forms ligand vacancies while partially retaining some ligands as structural pillars. The high density of ligand vacancies forms the active vacancy channel with abundant and highly-accessible undercoordinated Ni sites, exhibiting 5-25 fold and 20-400 fold activity enhancement compared to the hybrid pre-catalyst and standard β-Ni(OH)2 for the electrochemical oxidation of 25 different organic substrates, respectively. The tunable N-N ligand can also tailor the sizes of the vacancy channels to significantly impact the substrate configuration leading to unprecedented substrate-dependent reactivities on hydroxide/oxide catalysts. This approach bridges heterogenous and homogeneous catalysis for creating efficient and functional catalysis with enzyme-like properties.
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Affiliation(s)
- Zhe Chen
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Jili Li
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Lingshen Meng
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Jianan Li
- grid.28056.390000 0001 2163 4895National Engineering Laboratory for Industrial Wastewater Treatment, East China University of Science and Technology, Shanghai, 200237 China
| | - Yaming Hao
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Tao Jiang
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Xuejing Yang
- grid.28056.390000 0001 2163 4895National Engineering Laboratory for Industrial Wastewater Treatment, East China University of Science and Technology, Shanghai, 200237 China
| | - Yefei Li
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China.
| | - Zhi-Pan Liu
- grid.8547.e0000 0001 0125 2443Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438 China
| | - Ming Gong
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China.
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2
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Plapp BV, Gakhar L, Subramanian R. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Acta Crystallogr D Struct Biol 2022; 78:1221-1234. [PMID: 36189742 PMCID: PMC9527765 DOI: 10.1107/s2059798322008361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022] Open
Abstract
Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD+ and 2,2,2-trifluoroethanol were determined to 1.1-1.3 Å resolution below the `glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 Å2) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 Å2 for the overall complexes and of 5-10 Å2 for C4N of NAD+ and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of ∼0.3 Å and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD+ and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.
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Affiliation(s)
- Bryce V. Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
| | - Lokesh Gakhar
- Protein and Crystallography Facility, Carver College of Medicine, The University of Iowa, Iowa City, IA 52252, USA
| | - Ramaswamy Subramanian
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
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3
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Zheng D, Nakabayashi M, Asano Y. Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex. J Biol Chem 2022; 298:101650. [PMID: 35101448 PMCID: PMC8892092 DOI: 10.1016/j.jbc.2022.101650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/02/2022] Open
Abstract
Hydroxynitrile lyase from Linum usitatissimum (LuHNL) is an enzyme involved in the catabolism of cyanogenic glycosides to release hydrogen cyanide upon tissue damage. This enzyme strictly conserves the substrate- and NAD(H)-binding domains of Zn2+-containing alcohol dehydrogenase (ADH); however, there is no evidence suggesting that LuHNL possesses ADH activity. Herein, we determined the ligand-free 3D structure of LuHNL and its complex with acetone cyanohydrin and (R)-2-butanone cyanohydrin using X-ray crystallography. These structures reveal that an A-form NAD+ is tightly but not covalently bound to each subunit of LuHNL. The restricted movement of the NAD+ molecule is due to the "sandwich structure" on the adenine moiety of NAD+. Moreover, the structures and mutagenesis analysis reveal a novel reaction mechanism for cyanohydrin decomposition involving the cyano-zinc complex and hydrogen-bonded interaction of the hydroxyl group of cyanohydrin with Glu323/Thr65 and H2O/Lys162 of LuHNL. The deprotonated Lys162 and protonated Glu323 residues are presumably stabilized by a partially desolvated microenvironment. In summary, the substrate binding geometry of LuHNL provides insights into the differences in activities of LuHNL and ADH, and identifying this novel reaction mechanism is an important contribution to the study of hydroxynitrile lyases.
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Affiliation(s)
- Daijun Zheng
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Makoto Nakabayashi
- Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Osaka, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama, Japan.
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4
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Plapp BV, Subramanian R. Alternative binding modes in abortive NADH-alcohol complexes of horse liver alcohol dehydrogenase. Arch Biochem Biophys 2021; 701:108825. [PMID: 33675814 PMCID: PMC7980771 DOI: 10.1016/j.abb.2021.108825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 10/22/2022]
Abstract
Enzymes typically have high specificity for their substrates, but the structures of substrates and products differ, and multiple modes of binding are observed. In this study, high resolution X-ray crystallography of complexes with NADH and alcohols show alternative modes of binding in the active site. Enzyme crystallized with the good substrates NAD+ and 4-methylbenzyl alcohol was found to be an abortive complex of NADH with 4-methylbenzyl alcohol rotated to a "non-productive" mode as compared to the structures that resemble reactive Michaelis complexes with NAD+ and 2,2,2-trifluoroethanol or 2,3,4,5,6-pentafluorobenzyl alcohol. The NADH is formed by reduction of the NAD+ with the alcohol during the crystallization. The same structure was also formed by directly crystallizing the enzyme with NADH and 4-methylbenzyl alcohol. Crystals prepared with NAD+ and 4-bromobenzyl alcohol also form the abortive complex with NADH. Surprisingly, crystals prepared with NAD+ and the strong inhibitor 1H,1H-heptafluorobutanol also had NADH, and the alcohol was bound in two different conformations that illustrate binding flexibility. Oxidation of 2-methyl-2,4-pentanediol during the crystallization apparently led to reduction of the NAD+. Kinetic studies show that high concentrations of alcohols can bind to the enzyme-NADH complex and activate or inhibit the enzyme. Together with previous studies on complexes with NADH and formamide analogues of the carbonyl substrates, models for the Michaelis complexes with NAD+-alcohol and NADH-aldehyde are proposed.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242, USA.
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5
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Guntupalli SR, Li Z, Chang L, Plapp BV, Subramanian R. Cryo-Electron Microscopy Structures of Yeast Alcohol Dehydrogenase. Biochemistry 2021; 60:663-677. [PMID: 33620215 DOI: 10.1021/acs.biochem.0c00921] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structures of yeast alcohol dehydrogenase determined by X-ray crystallography show that the subunits have two different conformational states in each of the two dimers that form the tetramer. Apoenzyme and holoenzyme complexes relevant to the catalytic mechanism were described, but the asymmetry led to questions about the cooperativity of the subunits in catalysis. This study used cryo-electron microscopy (cryo-EM) to provide structures for the apoenzyme, two different binary complexes with NADH, and a ternary complex with NAD+ and 2,2,2-trifluoroethanol. All four subunits in each of these complexes are identical, as the tetramers have D2 symmetry, suggesting that there is no preexisting asymmetry and that the subunits can be independently active. The apoenzyme and one enzyme-NADH complex have "open" conformations and the inverted coordination of the catalytic zinc with Cys-43, His-66, Glu-67, and Cys-153, whereas another enzyme-NADH complex and the ternary complex have closed conformations with the classical coordination of the zinc with Cys-43, His-66, Cys-153, and a water or the oxygen of trifluoroethanol. The conformational change involves interactions of Arg-340 with the pyrophosphate group of the coenzyme and Glu-67. The cryo-EM and X-ray crystallography studies provide structures relevant for the catalytic mechanism.
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Affiliation(s)
- Sai Rohit Guntupalli
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.,Manipal University, Manipal, India.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Bryce V Plapp
- Department of Biochemistry, Bowen Science Building, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Ramaswamy Subramanian
- Department of Biological Sciences and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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6
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Kim K, Plapp BV. Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer. Biochemistry 2020; 59:862-879. [PMID: 31994873 DOI: 10.1021/acs.biochem.9b01074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous studies showed that the L57F and F93W alcohol dehydrogenases catalyze the oxidation of benzyl alcohol with some quantum mechanical hydrogen tunneling, whereas the V203A enzyme has diminished tunneling. Here, steady-state kinetics for the L57F and F93W enzymes were studied, and microscopic rate constants for the ordered bi-bi mechanism were estimated from simulations of transient kinetics for the S48T, F93A, S48T/F93A, F93W, and L57F enzymes. Catalytic efficiencies for benzyl alcohol oxidation (V1/EtKb) vary over a range of ∼100-fold for the less active enzymes up to the L57F enzyme and are mostly associated with the binding of alcohol rather than the rate constants for hydride transfer. In contrast, catalytic efficiencies for benzaldehyde reduction (V2/EtKp) are ∼500-fold higher for the L57F enzyme than for the less active enzymes and are mostly associated with the rate constants for hydride transfer. Atomic-resolution structures (1.1 Å) for the F93W and L57F enzymes complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol are almost identical to previous structures for the wild-type, S48T, and V203A enzymes. Least-squares refinement with SHELXL shows that the nicotinamide ring is slightly strained in all complexes and that the apparent donor-acceptor distances from C4N of NAD to C7 of pentafluorobenzyl alcohol range from 3.28 to 3.49 Å (±0.02 Å) and are not correlated with the rate constants for hydride transfer or hydrogen tunneling. How the substitutions affect the dynamics of reorganization during hydrogen transfer and the extent of tunneling remain to be determined.
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Affiliation(s)
- Keehyuk Kim
- Department of Biochemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
| | - Bryce V Plapp
- Department of Biochemistry , The University of Iowa , Iowa City , Iowa 52242 , United States
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7
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Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3'-Dephosphocoenzyme A. Arch Biochem Biophys 2018; 653:97-106. [PMID: 30018019 DOI: 10.1016/j.abb.2018.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 06/30/2018] [Accepted: 07/05/2018] [Indexed: 11/22/2022]
Abstract
Glu-267 is highly conserved in alcohol dehydrogenases and buried as a negatively-charged residue in a loop of the NAD coenzyme binding domain. Glu-267 might have a structural role and contribute to a rate-promoting vibration that facilitates catalysis. Substitutions of Glu-267 with histidine or asparagine residues increase the dissociation constants for the coenzymes (NAD+ by ∼40-fold, NADH by ∼200-fold) and significantly decrease catalytic efficiencies by 16-1200-fold various substrates and substituted enzymes. The turnover numbers modestly change with the substitutions, but hydride transfer is at least partially rate-limiting for turnover for alcohol oxidation. X-ray structures of the E267H and E267 N enzymes are similar to the apoenzyme (open) conformation of the wild-type enzyme, and the substitutions are accommodated by local changes in the structure. Surprisingly, the E267H and E267 N enzymes have endogenous (from the expression in E. coli) 3'-dephosphocoenzyme A bound in the active site with the ADP moiety in the NAD binding site and the pantethiene sulfhydryl bound to the catalytic zinc. The kinetics and crystallography show that the substitutions of Glu-267 hinder the conformational change, which occurs when wild-type enzyme binds coenzymes, and affect productive binding of substrates.
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8
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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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9
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Shanmuganatham KK, Wallace RS, Ting-I Lee A, Plapp BV. Contribution of buried distal amino acid residues in horse liver alcohol dehydrogenase to structure and catalysis. Protein Sci 2018; 27:750-768. [PMID: 29271062 DOI: 10.1002/pro.3370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 01/06/2023]
Abstract
The dynamics of enzyme catalysis range from the slow time scale (∼ms) for substrate binding and conformational changes to the fast time (∼ps) scale for reorganization of substrates in the chemical step. The contribution of global dynamics to catalysis by alcohol dehydrogenase was tested by substituting five different, conserved amino acid residues that are distal from the active site and located in the hinge region for the conformational change or in hydrophobic clusters. X-ray crystallography shows that the structures for the G173A, V197I, I220 (V, L, or F), V222I, and F322L enzymes complexed with NAD+ and an analogue of benzyl alcohol are almost identical, except for small perturbations at the sites of substitution. The enzymes have very similar kinetic constants for the oxidation of benzyl alcohol and reduction of benzaldehyde as compared to the wild-type enzyme, and the rates of conformational changes are not altered. Less conservative substitutions of these amino acid residues, such as G173(V, E, K, or R), V197(G, S, or T), I220(G, S, T, or N), and V222(G, S, or T) produced unstable or poorly expressed proteins, indicating that the residues are critical for global stability. The enzyme scaffold accommodates conservative substitutions of distal residues, and there is no evidence that fast, global dynamics significantly affect the rate constants for hydride transfers. In contrast, other studies show that proximal residues significantly participate in catalysis.
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Affiliation(s)
- Karthik K Shanmuganatham
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Diagnostic Virology Laboratory, USDA, Ames, IA, 50010
| | - Rachel S Wallace
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Ann Ting-I Lee
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109.,No 92, Jing Mao 1st Rd., Taichung, Taiwan, 406, Republic of China
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242-1109
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10
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Plapp BV, Savarimuthu BR, Ferraro DJ, Rubach JK, Brown EN, Ramaswamy S. Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis. Biochemistry 2017. [PMID: 28640600 PMCID: PMC5518280 DOI: 10.1021/acs.biochem.7b00446] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
During catalysis
by liver alcohol dehydrogenase (ADH), a water
bound to the catalytic zinc is replaced by the oxygen of the substrates.
The mechanism might involve a pentacoordinated zinc or a double-displacement
reaction with participation by a nearby glutamate residue, as suggested
by studies of human ADH3, yeast ADH1, and some other tetrameric ADHs.
Zinc coordination and participation of water in the enzyme mechanism
were investigated by X-ray crystallography. The apoenzyme and its
complex with adenosine 5′-diphosphoribose have an open protein
conformation with the catalytic zinc in one position, tetracoordinated
by Cys-46, His-67, Cys-174, and a water molecule. The bidentate chelators
2,2′-bipyridine and 1,10-phenanthroline displace the water
and form a pentacoordinated zinc. The enzyme–NADH complex has
a closed conformation similar to that of ternary complexes with coenzyme
and substrate analogues; the coordination of the catalytic zinc is
similar to that found in the apoenzyme, except that a minor, alternative
position for the catalytic zinc is ∼1.3 Å from the major
position and closer to Glu-68, which could form the alternative coordination
to the catalytic zinc. Complexes with NADH and N-1-methylhexylformamide
or N-benzylformamide (or with NAD+ and
fluoro alcohols) have the classical tetracoordinated zinc, and no
water is bound to the zinc or the nicotinamide rings. The major forms
of the enzyme in the mechanism have a tetracoordinated zinc, where
the carboxylate group of Glu-68 could participate in the exchange
of water and substrates on the zinc. Hydride transfer in the Michaelis
complexes does not involve a nearby water.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Baskar Raj Savarimuthu
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Daniel J Ferraro
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Jon K Rubach
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Eric N Brown
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - S Ramaswamy
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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11
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Abstract
Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.
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Affiliation(s)
- P Singh
- University of Iowa, Iowa City, IA, United States
| | - Z Islam
- University of Iowa, Iowa City, IA, United States
| | - A Kohen
- University of Iowa, Iowa City, IA, United States.
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12
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Lederer F, Vignaud C, North P, Bodevin S. Trifluorosubstrates as mechanistic probes for an FMN-dependent l-2-hydroxy acid-oxidizing enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1215-1221. [PMID: 27155230 DOI: 10.1016/j.bbapap.2016.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 11/29/2022]
Abstract
A controversy exists with respect to the mechanism of l-2-hydroxy acid oxidation by members of a family of FMN-dependent enzymes. A so-called carbanion mechanism was initially proposed, in which the active site histidine abstracts the substrate α-hydrogen as a proton, followed by electron transfer from the carbanion to the flavin. But an alternative mechanism was not incompatible with some results, a mechanism in which the active site histidine instead picks up the substrate hydroxyl proton and a hydride transfer occurs. Even though more recent experiments ruling out such a mechanism were published (Rao & Lederer (1999) Protein Science 7, 1531-1537), a few authors have subsequently interpreted their results with variant enzymes in terms of a hydride transfer. In the present work, we analyse the reactivity of trifluorolactate, a substrate analogue, with the flavocytochrome b2 (Fcb2) flavodehydrogenase domain, compared to its reactivity with an NAD-dependent lactate dehydrogenase (LDH), for which this compound is known to be an inhibitor (Pogolotti & Rupley (1973) Biochem. Biophys. Res. Commun, 55, 1214-1219). Indeed, electron attraction by the three fluorine atoms should make difficult the removal of the α-H as a hydride. We also analyse the reactivity of trifluoropyruvate with the FMN- and NAD-dependent enzymes. The results substantiate a different effect of the fluorine substituents on the two enzymes compared to their normal substrates. In the discussion we analyse the conclusions of recent papers advocating a hydride transfer mechanism for the family of l-2-hydroxy acid oxidizing FMN-dependent enzymes.
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Affiliation(s)
- Florence Lederer
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France; Laboratoire de Chimie Physique, CNRS UMR 8000, Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France.
| | - Caroline Vignaud
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Paul North
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Sabrina Bodevin
- Laboratoire d'Enzymologie, UPR 9063, CNRS, 91198 Gif-sur-Yvette Cedex, France
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13
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Pohanka M. Toxicology and the biological role of methanol and ethanol: Current view. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2015; 160:54-63. [PMID: 26006090 DOI: 10.5507/bp.2015.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/24/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alcohol variants such as ethanol and methanol are simple organic compounds widely used in foods, pharmaceuticals, chemical synthesis, etc. Both are becoming an emerging health problem; abuse of ethanol containing beverages can lead to disparate health problems and methanol is highly toxic and unfit for consumption. METHODS AND RESULTS This review summarizes the basic knowledge about ethanol and methanol toxicity, the effect mechanism on the body, the current care of poisoned individuals and the implication of alcohols in the development of diseases. Alcohol related dementia, stroke, metabolic syndrome and hepatitis are discussed as well. Besides ethanol, methanol toxicity and its biodegradation pathways are addressed. CONCLUSIONS The impact of ethanol and methanol on the body is shown as case reports, along with a discussion on the possible implication of alcohol in Alzheimer's disease and antidotal therapy for methanol poisoning. The role of ethanol in cancer and degenerative disorders seems to be underestimated given the current knowledge. Treatment in case of poisoning is another issue that remains unresolved even though effective protocols and drugs exist.
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Affiliation(s)
- Miroslav Pohanka
- Faculty of Military Health Sciences, University of Defense, Trebesska 1575, Hradec Kralove, Czech Republic
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14
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Raj S, Ramaswamy S, Plapp BV. Yeast alcohol dehydrogenase structure and catalysis. Biochemistry 2014; 53:5791-803. [PMID: 25157460 PMCID: PMC4165444 DOI: 10.1021/bi5006442] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/22/2014] [Indexed: 11/30/2022]
Abstract
Yeast (Saccharomyces cerevisiae) alcohol dehydrogenase I (ADH1) is the constitutive enzyme that reduces acetaldehyde to ethanol during the fermentation of glucose. ADH1 is a homotetramer of subunits with 347 amino acid residues. A structure for ADH1 was determined by X-ray crystallography at 2.4 Å resolution. The asymmetric unit contains four different subunits, arranged as similar dimers named AB and CD. The unit cell contains two different tetramers made up of "back-to-back" dimers, AB:AB and CD:CD. The A and C subunits in each dimer are structurally similar, with a closed conformation, bound coenzyme, and the oxygen of 2,2,2-trifluoroethanol ligated to the catalytic zinc in the classical tetrahedral coordination with Cys-43, Cys-153, and His-66. In contrast, the B and D subunits have an open conformation with no bound coenzyme, and the catalytic zinc has an alternative, inverted coordination with Cys-43, Cys-153, His-66, and the carboxylate of Glu-67. The asymmetry in the dimeric subunits of the tetramer provides two structures that appear to be relevant for the catalytic mechanism. The alternative coordination of the zinc may represent an intermediate in the mechanism of displacement of the zinc-bound water with alcohol or aldehyde substrates. Substitution of Glu-67 with Gln-67 decreases the catalytic efficiency by 100-fold. Previous studies of structural modeling, evolutionary relationships, substrate specificity, chemical modification, and site-directed mutagenesis are interpreted more fully with the three-dimensional structure.
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Affiliation(s)
| | | | - Bryce V. Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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