1
|
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.
Collapse
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
| |
Collapse
|
2
|
Warshel A, Bora RP. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 2017; 144:180901. [PMID: 27179464 DOI: 10.1063/1.4947037] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.
Collapse
Affiliation(s)
- Arieh Warshel
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| | - Ram Prasad Bora
- Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA
| |
Collapse
|
3
|
Yahashiri A, Rubach JK, Plapp BV. Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry 2014; 53:881-94. [PMID: 24437493 PMCID: PMC3969020 DOI: 10.1021/bi401583f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
A role
for protein dynamics in enzymatic catalysis of hydrogen
transfer has received substantial scientific support, but the connections
between protein structure and catalysis remain to be established.
Valine residues 203 and 207 are at the binding site for the nicotinamide
ring of the coenzyme in liver alcohol dehydrogenase and have been
suggested to facilitate catalysis with “protein-promoting vibrations”
(PPV). We find that the V207A substitution has small effects on steady-state
kinetic constants and the rate of hydrogen transfer; the introduced
cavity is empty and is tolerated with minimal effects on structure
(determined at 1.2 Å for the complex with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to
support a role for Val-207 in the dynamics of catalysis. The protein
structures and ligand geometries (including donor–acceptor
distances) in the V203A enzyme complexed with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined
at 1.1 Å) are very similar to those for the wild-type enzyme,
except that the introduced cavity accommodates a new water molecule
that contacts the nicotinamide ring. The structures of the V203A enzyme
complexes suggest, in contrast to previous studies, that the diminished
tunneling and decreased rate of hydride transfer (16-fold, relative
to that of the wild-type enzyme) are not due to differences in ground-state
ligand geometries. The V203A substitution may alter the PPV and the
reorganization energy for hydrogen transfer, but the protein scaffold
and equilibrium thermal motions within the Michaelis complex may be
more significant for enzyme catalysis.
Collapse
Affiliation(s)
- Atsushi Yahashiri
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242-1109, United States
| | | | | |
Collapse
|
4
|
Kamerlin SCL, Warshel A. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis? Proteins 2010; 78:1339-75. [PMID: 20099310 PMCID: PMC2841229 DOI: 10.1002/prot.22654] [Citation(s) in RCA: 356] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, the transcription, and translation of genetic information, and signaling. They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. This review examines the dynamical proposal in a critical way, considering basically all reasonable definitions, including (but not limited to) such proposed effects as "coupling between conformational and chemical motions," "landscape searches" and "entropy funnels." It is shown that none of these proposed effects have been experimentally demonstrated to contribute to catalysis, nor are they supported by consistent theoretical studies. On the other hand, it is clarified that careful simulation studies have excluded most (if not all) dynamical proposals. This review places significant emphasis on clarifying the role of logical definitions of different catalytic proposals, and on the need for a clear formulation in terms of the assumed potential surface and reaction coordinate. Finally, it is pointed out that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes, through the corresponding changes in the activation free energies.
Collapse
Affiliation(s)
- Shina C. L. Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles CA-90089, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles CA-90089, USA
| |
Collapse
|
5
|
Kamerlin SCL, Mavri J, Warshel A. Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues. FEBS Lett 2010; 584:2759-66. [PMID: 20433839 DOI: 10.1016/j.febslet.2010.04.062] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 04/21/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
The idea that tunneling is enhanced by the compression of the donor-acceptor distance has attracted significant interest. In particular, recent studies argued that this proposal is consistent with pressure effects on enzymatic reactions, and that the observed pressure effects support the idea of vibrationally enhanced catalysis. However, a careful analysis of the current works reveals serious inconsistencies in the evidence presented to support these hypotheses. Apparently, tunneling decreases upon compression, and external pressure does not lead to the applicable compression of the free energy surface. Additionally, pressure experiments do not provide actual evidence for vibrationally enhanced catalysis. Finally, the temperature dependence of the entropy change in hydride transfer reactions is shown to reflect simple electrostatic effects.
Collapse
|
6
|
Kamerlin SCL, Warshel A. An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling. J PHYS ORG CHEM 2010; 23:677-684. [PMID: 21494414 DOI: 10.1002/poc.1620] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles CA-90089, USA
| | | |
Collapse
|
7
|
Bruice TC. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. Chem Rev 2007; 106:3119-39. [PMID: 16895321 DOI: 10.1021/cr050283j] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Thomas C Bruice
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA.
| |
Collapse
|
8
|
Liu H, Warshel A. Origin of the Temperature Dependence of Isotope Effects in Enzymatic Reactions: The Case of Dihydrofolate Reductase. J Phys Chem B 2007; 111:7852-61. [PMID: 17571875 DOI: 10.1021/jp070938f] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The origin of the temperature dependence of kinetic isotope effects (KIEs) in enzyme reactions is a problem of general interest and a major challenge for computational chemistry. The present work simulates the nuclear quantum mechanical (NQM) effects and the corresponding KIE in dihydrofolate reductase (DHFR) and two of its mutants by using the empirical valence bond (EVB) and the quantum classical path (QCP) centroid path integral approach. Our simulations reproduce the overall observed trend while using a fully microscopic rather than a phenomenological picture and provide an interesting insight. It appears that the KIE increases when the distance between the donor and acceptor increases, in a somewhat counter intuitive way. The temperature dependence of the KIE appears to reflect mainly the temperature dependence of the distance between the donor and acceptor. This trend is also obtained from a simplified vibronic treatment, but as demonstrated here, the vibronic treatment is not valid at short and medium distances, where it is essential to use the path integral or other approaches capable of moving seamlessly from the adiabatic to the diabatic limits. It is pointed out that although the NQM effects do not contribute to catalysis in DHFR, the observed temperature dependence can be used to refine the potential of mean force for the donor and acceptor distance and its change due to distanced mutations.
Collapse
Affiliation(s)
- Hanbin Liu
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
| | | |
Collapse
|
9
|
Luo J, Bruice TC. Low-frequency normal modes in horse liver alcohol dehydrogenase and motions of residues involved in the enzymatic reaction. Biophys Chem 2007; 126:80-5. [PMID: 16737770 DOI: 10.1016/j.bpc.2006.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 05/10/2006] [Indexed: 11/18/2022]
Abstract
Normal mode analysis using the elastic network model has provided characteristics and directions of the low-frequency large domain motions of horse liver alcohol dehydrogenase. Three normal modes (mode 1, mode 7, and mode 8) were identified as representative domain motions that may promote the onset of Near Attack Conformers or facilitate the product to be released. The pattern of the atomic displacement for some key residues (such as Val292 and Val203) revealed in this study is in line with experimental structural and kinetic studies and theoretical simulations.
Collapse
Affiliation(s)
- Jia Luo
- Department of Chemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
10
|
Antoniou D, Basner J, Núñez S, Schwartz SD. Effect of enzyme dynamics on catalytic activity. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0065-3160(06)41006-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
11
|
Luo J, Bruice TC. Anticorrelated motions as a driving force in enzyme catalysis: the dehydrogenase reaction. Proc Natl Acad Sci U S A 2004; 101:13152-6. [PMID: 15331786 PMCID: PMC516540 DOI: 10.1073/pnas.0405502101] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics and cross-correlation analysis of the horse liver alcohol dehydrogenase HLADH.NAD(+).PhCH(2)O(-) complex has established anticorrelated motions between the NAD(+)-binding domain and other portions of the enzyme. Four pairs of anticorrelated interactions are (i and ii) cofactor-binding domain: C(alpha) of V292 and the CG1 of V203 with C7 of PhCH(2)O(-); (iii) cofactor-binding domain: amide carbonyl oxygen of I318 with amide N of H67; and (iv) cofactor domain: C(alpha) of T178 with carbonyl oxygen of L141. The average distances between pairs are 9.2 A for i, 8.2 A for ii, 14.7 A for iii, and 18.2 A for iv. The motions of i and ii are most important in the approximately 0.5 A pushing of C4 of NAD(+) toward C7 of PhCH(2)O(-) to form push near-attack conformer (NACs). The motions of iv are less so, and those of iii are not important. Seventy-five quantum mechanics/molecular mechanics calculations of the energies of reaction were carried out without structural restrictions from different stages of the molecular dynamics trajectory. Of the 71 conformations, the 29 fulfilling NAC criteria were associated with the lowest energies of activation. Thus, anticorrelated motions from the NAD(+)-binding domain by way of the neighboring V292 and V203 have a pushing motion, which moves the C4 of NAD(+) toward the H-C7 of the substrate. Longer-range anticorrelated motions involving the cofactor-binding domain have no or very little influence on NAC formation.
Collapse
Affiliation(s)
- Jia Luo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
12
|
Jarczewski A, Hubbard CD. A review of proton transfer reactions between various carbon-acids and amine bases in aprotic solvents. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(03)00086-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
13
|
Luo J, Bruice TC. Ten-nanosecond molecular dynamics simulation of the motions of the horse liver alcohol dehydrogenase.PhCH2O- complex. Proc Natl Acad Sci U S A 2002; 99:16597-600. [PMID: 12481026 PMCID: PMC139189 DOI: 10.1073/pnas.262667599] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations have been carried out for a period of 10 ns with the dimeric enzyme horse liver alcohol dehydrogenase (HLADH) present as the reactive complex HLADH.NAD+. PhCH2O-. Cross-correlation analysis of the trajectory was carried out with the latter from 500 ps to 10 ns. The resulting cross-correlation map allowed the identification of the correlated and anticorrelated motions, which involve the entire protein. Anticorrelated and correlated motions are carried into the active site-aligned residues.
Collapse
Affiliation(s)
- Jia Luo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
14
|
Antoniou D, Caratzoulas S, Kalyanaraman C, Mincer JS, Schwartz SD. Barrier passage and protein dynamics in enzymatically catalyzed reactions. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:3103-12. [PMID: 12084050 DOI: 10.1046/j.1432-1033.2002.03021.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This review describes studies of particular enzymatically catalyzed reactions to investigate the possibility that catalysis is mediated by protein dynamics. That is, evolution has crafted the protein backbone of the enzyme to direct vibrations in such a fashion to speed reaction. The review presents the theoretical approach we have used to investigate this problem, but it is designed for the nonspecialist. The results show that in alcohol dehydrogenase, dynamic protein motion is in fact strongly coupled to chemical reaction in such a way as to promote catalysis. This result is in concert with both experimental data and interpretations for this and other enzyme systems studied in the laboratories of the two other investigators who have published reviews in this issue.
Collapse
Affiliation(s)
- Dimitri Antoniou
- Department of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | | | | | | | | |
Collapse
|
15
|
Billeter SR, Webb SP, Agarwal PK, Iordanov T, Hammes-Schiffer S. Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion. J Am Chem Soc 2001; 123:11262-72. [PMID: 11697969 DOI: 10.1021/ja011384b] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The quantum dynamics of the hydride transfer reaction catalyzed by liver alcohol dehydrogenase (LADH) are studied with real-time dynamical simulations including the motion of the entire solvated enzyme. The electronic quantum effects are incorporated with an empirical valence bond potential, and the nuclear quantum effects of the transferring hydrogen are incorporated with a mixed quantum/classical molecular dynamics method in which the transferring hydrogen nucleus is represented by a three-dimensional vibrational wave function. The equilibrium transition state theory rate constants are determined from the adiabatic quantum free energy profiles, which include the free energy of the zero point motion for the transferring nucleus. The nonequilibrium dynamical effects are determined by calculating the transmission coefficients with a reactive flux scheme based on real-time molecular dynamics with quantum transitions (MDQT) surface hopping trajectories. The values of nearly unity for these transmission coefficients imply that nonequilibrium dynamical effects such as barrier recrossings are not dominant for this reaction. The calculated deuterium and tritium kinetic isotope effects for the overall rate agree with experimental results. These simulations elucidate the fundamental nature of the nuclear quantum effects and provide evidence of hydrogen tunneling in the direction along the donor-acceptor axis. An analysis of the geometrical parameters during the equilibrium and nonequilibrium simulations provides insight into the relation between specific enzyme motions and enzyme activity. The donor-acceptor distance, the catalytic zinc-substrate oxygen distance, and the coenzyme (NAD(+)/NADH) ring angles are found to strongly impact the activation free energy barrier, while the donor-acceptor distance and one of the coenzyme ring angles are found to be correlated to the degree of barrier recrossing. The distance between VAL-203 and the reactive center is found to significantly impact the activation free energy but not the degree of barrier recrossing. This result indicates that the experimentally observed effect of mutating VAL-203 on the enzyme activity is due to the alteration of the equilibrium free energy difference between the transition state and the reactant rather than nonequilibrium dynamical factors. The promoting motion of VAL-203 is characterized in terms of steric interactions involving THR-178 and the coenzyme.
Collapse
Affiliation(s)
- S R Billeter
- Department of Chemistry, 152 Davey Laboratory, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | | | | | | |
Collapse
|
16
|
Alhambra C, Corchado J, Sánchez ML, Garcia-Viloca M, Gao J, Truhlar DG. Canonical Variational Theory for Enzyme Kinetics with the Protein Mean Force and Multidimensional Quantum Mechanical Tunneling Dynamics. Theory and Application to Liver Alcohol Dehydrogenase. J Phys Chem B 2001. [DOI: 10.1021/jp0120312] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cristóbal Alhambra
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - José Corchado
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Maria Luz Sánchez
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Mireia Garcia-Viloca
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| |
Collapse
|
17
|
Svensson S, Strömberg P, Sandalova T, Höög J. Class II alcohol dehydrogenase (ADH2)--adding the structure. Chem Biol Interact 2001; 130-132:339-50. [PMID: 11306056 DOI: 10.1016/s0009-2797(00)00276-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Class II alcohol dehydrogenase (ADH2) represents a highly divergent class of alcohol dehydrogenases predominantly found in liver. Several species variants of ADH2 have been described, and the rodent enzymes form a functionally distinct subgroup with interesting catalytic properties. First, as compared with other ADHs, the catalytic efficiency is low for this subgroup. Second, the substrate repertoire is unique, e.g. rodent ADH2s are not saturated with ethanol as substrate, and while omega-hydroxy fatty acids are common substrates for the human ADH1-ADH4 isoenzymes, including ADH2, these compounds function as inhibitors rather than substrates. The recently determined structure of mouse ADH2 reveals a novel substrate-pocket topography that accounts for the observed substrate specificity and may, therefore, be important for the exploration of orphan substrates of ADH2. It is possible to improve the catalytic efficiency of mouse ADH2 by an array of mutations at position 47. Residue Pro47 of the wild type ADH2 enzyme seems to strain the binding of coenzyme, which prevents a close approach between the coenzyme and substrate for efficient hydrogen transfer. Based on crystallographic and mechanistic investigations, the effects of residue replacements at position 47 are multiple, affecting the distance for hydride transfer, the pK(a) of the bound alcohol substrate as well as the affinity for coenzyme.
Collapse
Affiliation(s)
- S Svensson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | | | | | | |
Collapse
|