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Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation. Int J Mol Sci 2022; 23:ijms231911140. [PMID: 36232441 PMCID: PMC9569753 DOI: 10.3390/ijms231911140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The metal binding at protein–protein interfaces is still uncharted territory in intermolecular interactions. To date, only a few protein complexes binding Zn(II) in an intermolecular manner have been deeply investigated. The most notable example of such interfaces is located in the highly conserved Rad50 protein, part of the Mre11-Rad50-Nbs1 (MRN) complex, where Zn(II) is required for homodimerization (Zn(Rad50)2). The high stability of Zn(Rad50)2 is conserved not only for the protein derived from the thermophilic archaeon Pyrococcus furiosus (logK12 = 20.95 for 130-amino-acid-long fragment), which was the first one studied, but also for the human paralog studied here (logK12 = 19.52 for a 183-amino-acid-long fragment). As we reported previously, the extremely high stability results from the metal-coupled folding process where particular Rad50 protein fragments play a critical role. The sequence–structure–stability analysis based on human Rad50 presented here separates the individual structural components that increase the stability of the complex, pointing to amino acid residues far away from the Zn(II) binding site as being largely responsible for the complex stabilization. The influence of the individual components is very well reflected by the previously published crystal structure of the human Rad50 zinc hook (PDB: 5GOX). In addition, we hereby report the effect of phosphorylation of the zinc hook domain, which exerts a destabilizing effect on the domain. This study identifies factors governing the stability of metal-mediated protein–protein interactions and illuminates their molecular basis.
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2
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Dinh T, Rahn KT, Phillips RS. Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from
Thermoanaerobacter pseudoethanolicus
reveal the dynamics of ligand exchange and the proton relay network. Proteins 2022; 90:1570-1583. [DOI: 10.1002/prot.26339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tung Dinh
- Department of Chemistry University of Georgia Athens Georgia USA
| | - K. Troy Rahn
- Department of Chemistry University of Georgia Athens Georgia USA
| | - Robert S. Phillips
- Department of Chemistry University of Georgia Athens Georgia USA
- Department of Biochemistry and Molecular Biology University of Georgia Athens Georgia USA
- Center for Metalloenzyme Studies University of Georgia Athens Georgia USA
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3
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Martins FL, Pordea A, Jäger CM. Computationally driven design of an artificial metalloenzyme using supramolecular anchoring strategies of iridium complexes to alcohol dehydrogenase. Faraday Discuss 2022; 234:315-335. [PMID: 35156975 DOI: 10.1039/d1fd00070e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Artificial metalloenzymes (ArMs) confer non-biological reactivities to biomolecules, whilst taking advantage of the biomolecular architecture in terms of their selectivity and renewable origin. In particular, the design of ArMs by the supramolecular anchoring of metal catalysts to protein hosts provides flexible and easy to optimise systems. The use of cofactor dependent enzymes as hosts gives the advantage of both a (hydrophobic) binding site for the substrate and a cofactor pocket to accommodate the catalyst. Here, we present a computationally driven design approach of ArMs for the transfer hydrogenation reaction of cyclic imines, starting from the NADP+-dependent alcohol dehydrogenase from Thermoanaerobacter brockii (TbADH). We tested and developed a molecular docking workflow to define and optimize iridium catalysts with high affinity for the cofactor binding site of TbADH. The workflow uses high throughput docking of compound libraries to identify key structural motifs for high affinity, followed by higher accuracy docking methods on smaller, focused ligand and catalyst libraries. Iridium sulfonamide catalysts were selected and synthesised, containing either a triol, a furane, or a carboxylic acid to provide the interaction with the cofactor binding pocket. IC50 values of the resulting complexes during TbADH-catalysed alcohol oxidation were determined by competition experiments and were between 4.410 mM and 0.052 mM, demonstrating the affinity of the iridium complexes for either the substrate or the cofactor binding pocket of TbADH. The catalytic activity of the free iridium complexes in solution showed a maximal turnover number (TON) of 90 for the reduction of salsolidine by the triol-functionalised iridium catalyst, whilst in the presence of TbADH, only the iridium catalyst with the triol anchoring functionality showed activity for the same reaction (TON of 36 after 24 h). The observation that the artificial metalloenzymes developed here lacked stereoselectivity demonstrates the need for the further investigation and optimisation of the ArM. Our results serve as a starting point for the design of robust artificial metalloenzymes, exploiting supramolecular anchoring to natural NAD(P)H binding pockets.
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Affiliation(s)
- Floriane L Martins
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, UK.
| | - Anca Pordea
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, UK.
| | - Christof M Jäger
- Sustainable Process Technologies, Faculty of Engineering, University of Nottingham, Nottingham, UK.
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4
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Kim K, Plapp BV. Substitution of cysteine-153 ligated to the catalytic zinc in yeast alcohol dehydrogenase with aspartic acid and analysis of mechanisms of related medium chain dehydrogenases. Chem Biol Interact 2019; 302:172-182. [PMID: 30721696 DOI: 10.1016/j.cbi.2019.01.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 01/14/2019] [Accepted: 01/31/2019] [Indexed: 11/28/2022]
Abstract
The catalytic zincs in complexes of horse liver and yeast alcohol dehydrogenases (ADH) with NAD+ and the substrate analogue, 2,2,2-trifluoroethanol, are ligated to two cysteine residues and one histidine residue from the protein and the oxygen from the alcohol. The zinc facilitates deprotonation of the alcohol and is essential for catalysis. In the yeast apoenzyme, the zinc is coordinated to a nearby glutamic acid, which is displaced by the alcohol in the complex with NAD+. Some homologous medium chain dehydrogenases have a cysteine replaced by aspartic or glutamic acid residues. How an aspartic acid would affect catalysis was studied by replacing Cys-153 in Saccharomyces cerevisiae ADH1 by using site-directed mutagenesis. The C153D enzyme was about as stable as the wild-type enzyme, if EDTA was not included in the buffers. The substitution increased affinity for NAD+ by 3-fold, but did not affect NADH binding. At pH 7.3, the turnover number for ethanol oxidation (V1/Et) decreased by 7-fold and catalytic efficiency decreased 18-fold (V1/EtKb), but turnover for acetaldehyde reduction (V2/Et) was the same as for wild-type enzyme and catalytic efficiency decreased 8-fold (V2/EtKp). Deuterium isotope effects of 3.0 on V1/Et and 3.8 on V1/EtKb for ethanol oxidation suggest that hydride transfer is more rate-limiting for turnover for the C153D enzyme than by wild-type enzyme. The patterns of pH dependence for V1/EtKb for ethanol oxidation were similar for both enzymes in the pH range from 7 to 9. The C153D substitution decreased binding of trifluoroethanol by 5-fold and of pyrazole by 65-fold. Substrate specificities for C153D and wild-type ADHs for primary alcohols have similar patterns. Efficiency for secondary alcohols decreased only about 4-fold, and efficiencies for 1,2-propanediol and acetone were about the same as for wild-type enzyme. The C153D substitution modestly affects catalysis by altering ligand exchange on the zinc or local structure. Structures and mechanisms for acid-base catalysis in related medium chain dehydrogenases with substitutions of the homologous cysteine are reviewed and analyzed.
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Affiliation(s)
- Keehyuk Kim
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242, USA.
| | - Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA, 52242, USA.
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5
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Moa S, Himo F. Quantum chemical study of mechanism and stereoselectivity of secondary alcohol dehydrogenase. J Inorg Biochem 2017; 175:259-266. [PMID: 28803132 DOI: 10.1016/j.jinorgbio.2017.07.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/02/2017] [Accepted: 07/18/2017] [Indexed: 11/17/2022]
Abstract
Secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) is a Zn- and NADP-dependent enzyme that catalyses the reversible transformation of secondary alcohols into ketones. It is of potential biocatalytic interest as it can be used in the synthesis of chiral alcohols by asymmetric reduction of ketones. In this paper, density functional theory calculations are employed to elucidate the origins of the enantioselectivity of TbSADH using a large model of the active site and considering two different substrates, 2-butanol and 3-hexanol. For these two substrates the enzyme has experimentally been shown to have the opposite enantioselectivity. The energy profiles for the reactions are calculated and the stationary points along the reaction path are characterised. The calculations first confirm that the general mechanism proposed for other alcohol dehydrogenases is energetically viable. In this mechanism, a proton is first transferred from the substrate to a histidine residue at the surface, followed by a hydride transfer to the NADP cofactor. The calculated overall energy barrier is consistent with the measured rate constant. Very importantly, the calculations are able to reproduce and rationalise the enantioselectivity of the enzyme for both substrates. The detailed characterisation of the energies and geometries of the involved transition states will be valuable in the rational engineering of TbSADH to expand its utility in biocatalysis.
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Affiliation(s)
- Sara Moa
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.
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6
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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
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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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7
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Benavente R, Esteban-Torres M, Kohring GW, Cortés-Cabrera Á, Sánchez-Murcia PA, Gago F, Acebrón I, de las Rivas B, Muñoz R, Mancheño JM. Enantioselective oxidation of galactitol 1-phosphate by galactitol-1-phosphate 5-dehydrogenase from Escherichia coli. ACTA ACUST UNITED AC 2015; 71:1540-54. [PMID: 26143925 DOI: 10.1107/s1399004715009281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/15/2015] [Indexed: 11/11/2022]
Abstract
Galactitol-1-phosphate 5-dehydrogenase (GPDH) is a polyol dehydrogenase that belongs to the medium-chain dehydrogenase/reductase (MDR) superfamily. It catalyses the Zn(2+)- and NAD(+)-dependent stereoselective dehydrogenation of L-galactitol 1-phosphate to D-tagatose 6-phosphate. Here, three crystal structures of GPDH from Escherichia coli are reported: that of the open state of GPDH with Zn(2+) in the catalytic site and those of the closed state in complex with the polyols Tris and glycerol, respectively. The closed state of GPDH reveals no bound cofactor, which is at variance with the conformational transition of the prototypical mammalian liver alcohol dehydrogenase. The main intersubunit-contacting interface within the GPDH homodimer presents a large internal cavity that probably facilitates the relative movement between the subunits. The substrate analogue glycerol bound within the active site partially mimics the catalytically relevant backbone of galactitol 1-phosphate. The glycerol binding mode reveals, for the first time in the polyol dehydrogenases, a pentacoordinated zinc ion in complex with a polyol and also a strong hydrogen bond between the primary hydroxyl group and the conserved Glu144, an interaction originally proposed more than thirty years ago that supports a catalytic role for this acidic residue.
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Affiliation(s)
- Rocío Benavente
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - María Esteban-Torres
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Gebäude A1.5, 66123 Saarbruecken, Germany
| | - Álvaro Cortés-Cabrera
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Pedro A Sánchez-Murcia
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Federico Gago
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
| | - Iván Acebrón
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Blanca de las Rivas
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Rosario Muñoz
- Laboratory of Bacterial Biotechnology, Institute of Food Science and Technology and Nutrition (ICTAN), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | - José M Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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8
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Dhoke GV, Davari MD, Schwaneberg U, Bocola M. QM/MM Calculations Revealing the Resting and Catalytic States in Zinc-Dependent Medium-Chain Dehydrogenases/Reductases. ACS Catal 2015. [DOI: 10.1021/cs501524k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Gaurao V. Dhoke
- RWTH Aachen University, Chair of Biotechnology, Worringer Weg 3, D-52074 Aachen, Germany
| | - Mehdi D. Davari
- RWTH Aachen University, Chair of Biotechnology, Worringer Weg 3, D-52074 Aachen, Germany
| | - Ulrich Schwaneberg
- RWTH Aachen University, Chair of Biotechnology, Worringer Weg 3, D-52074 Aachen, Germany
| | - Marco Bocola
- RWTH Aachen University, Chair of Biotechnology, Worringer Weg 3, D-52074 Aachen, Germany
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9
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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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10
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Kang C, Hayes R, Sanchez EJ, Webb BN, Li Q, Hooper T, Nissen MS, Xun L. Furfural reduction mechanism of a zinc-dependent alcohol dehydrogenase from Cupriavidus necator JMP134. Mol Microbiol 2011; 83:85-95. [PMID: 22081946 DOI: 10.1111/j.1365-2958.2011.07914.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
FurX is a tetrameric Zn-dependent alcohol dehydrogenase (ADH) from Cupriavidus necator JMP134. The enzyme rapidly reduces furfural with NADH as the reducing power. For the first time among characterized ADHs, the high-resolution structures of all reaction steps were obtained in a time-resolved manner, thereby illustrating the complete catalytic events of NADH-dependent reduction of furfural and the dynamic Zn(2+) coordination among Glu66, water, substrate and product. In the fully closed conformation of the NADH complex, the catalytic turnover proved faster than observed for the partially closed conformation due to an effective proton transfer network. The domain motion triggered by NAD(H) association/dissociation appeared to facilitate dynamic interchanges in Zn(2+) coordination with substrate and product molecules, ultimately increasing the enzymatic turnover rate. NAD(+) dissociation appeared to be a slow process, involving multiple steps in concert with a domain opening and reconfiguration of Glu66. This agrees with the report that the cofactor is not dissociated from FurX during ethanol-dependent reduction of furfural, in which ethanol reduces NAD(+) to NADH that is subsequently used for furfural reduction.
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Affiliation(s)
- ChulHee Kang
- School of Molecular Biosciences Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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11
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Weckbecker A, Hummel W. Cloning, expression, and characterization of an (R)-specific alcohol dehydrogenase fromLactobacillus kefir. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420600893827] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Plapp BV. Conformational changes and catalysis by alcohol dehydrogenase. Arch Biochem Biophys 2009; 493:3-12. [PMID: 19583966 DOI: 10.1016/j.abb.2009.07.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/01/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
As shown by X-ray crystallography, horse liver alcohol dehydrogenase undergoes a global conformational change upon binding of NAD(+) or NADH, involving a rotation of the catalytic domain relative to the coenzyme binding domain and the closing up of the active site to produce a catalytically efficient enzyme. The conformational change requires a complete coenzyme and is affected by various chemical or mutational substitutions that can increase the catalytic turnover by altering the kinetics of the isomerization and rate of dissociation of coenzymes. The binding of NAD(+) is kinetically limited by a unimolecular isomerization (corresponding to the conformational change) that is controlled by deprotonation of the catalytic zinc-water to produce a negatively-charged zinc-hydroxide, which can attract the positively-charged nicotinamide ring. The deprotonation is facilitated by His-51 acting through a hydrogen-bonded network to relay the proton to solvent. Binding of NADH also involves a conformational change, but the rate is very fast. After the enzyme binds NAD(+) and closes up, the substrate displaces the hydroxide bound to the catalytic zinc; this exchange may involve a double displacement reaction where the carboxylate group of a glutamate residue first displaces the hydroxide (inverting the tetrahedral coordination of the zinc), and then the exogenous ligand displaces the glutamate. The resulting enzyme-NAD(+)-alcoholate complex is poised for hydrogen transfer, and small conformational fluctuations may bring the reactants together so that the hydride ion is transferred by quantum mechanical tunneling. In the process, the nicotinamide ring may become puckered, as seen in structures of complexes of the enzyme with NADH. The conformational changes of alcohol dehydrogenase demonstrate the importance of protein dynamics in catalysis.
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Affiliation(s)
- Bryce V Plapp
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242-1109, USA.
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13
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Youn B, Camacho R, Moinuddin SGA, Lee C, Davin LB, Lewis NG, Kang C. Crystal structures and catalytic mechanism of the Arabidopsis cinnamyl alcohol dehydrogenases AtCAD5 and AtCAD4. Org Biomol Chem 2006; 4:1687-97. [PMID: 16633561 DOI: 10.1039/b601672c] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cinnamyl alcohol dehydrogenase (CAD) multigene family in planta encodes proteins catalyzing the reductions of various phenylpropenyl aldehyde derivatives in a substrate versatile manner, and whose metabolic products are the precursors of structural lignins, health-related lignans, and various other metabolites. In Arabidopsis thaliana, the two isoforms, AtCAD5 and AtCAD4, are the catalytically most active being viewed as mainly involved in the formation of guaiacyl/syringyl lignins. In this study, we determined the crystal structures of AtCAD5 in the apo-form and as a binary complex with NADP+, respectively, and modeled that of AtCAD4. Both AtCAD5 and AtCAD4 are dimers with two zinc ions per subunit and belong to the Zn-dependent medium chain dehydrogenase/reductase (MDR) superfamily, on the basis of their overall 2-domain structures and distribution of secondary structural elements. The catalytic Zn2+ ions in both enzymes are tetrahedrally coordinated, but differ from those in horse liver alcohol dehydrogenase since the carboxyl side-chain of Glu70 is ligated to Zn2+ instead of water. Using AtCAD5, site-directed mutagenesis of Glu70 to alanine resulted in loss of catalytic activity, thereby indicating that perturbation of the Zn2+ coordination was sufficient to abolish catalytic activity. The substrate-binding pockets of both AtCAD5 and AtCAD4 were also examined, and found to be significantly different and smaller compared to that of a putative aspen sinapyl alcohol dehydrogenase (SAD) and a putative yeast CAD. While the physiological roles of the aspen SAD and the yeast CAD are uncertain, they nevertheless have a high similarity in the overall 3D structures to AtCAD5 and 4. With the bona fide CAD's from various species, nine out of the twelve residues which constitute the proposed substrate-binding pocket were, however, conserved. This is provisionally considered as indicative of a characteristic fingerprint for the CAD family.
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Affiliation(s)
- Buhyun Youn
- School of Molecular Biosciences, Washington State University, Pullman, 99164-4660, USA
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