51
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Li A, Ye L, Wu H, Yang X, Yu H. Characterization of an excellent anti-Prelog short-chain dehydrogenase/reductase EbSDR8 from Empedobacter brevis ZJUY-1401. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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52
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Büsing I, Höffken HW, Breuer M, Wöhlbrand L, Hauer B, Rabus R. Molecular Genetic and Crystal Structural Analysis of 1-(4-Hydroxyphenyl)-Ethanol Dehydrogenase from 'Aromatoleum aromaticum' EbN1. J Mol Microbiol Biotechnol 2015; 25:327-39. [PMID: 26488297 DOI: 10.1159/000439113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The dehydrogenation of 1-(4-hydroxyphenyl)-ethanol to 4-hydroxyacetophenone represents the second reaction step during anaerobic degradation of p-ethylphenol in the denitrifying bacterium 'Aromatoleum aromaticum' EbN1. Previous proteogenomic studies identified two different proteins (ChnA and EbA309) as possible candidates for catalyzing this reaction [Wöhlbrand et al: J Bacteriol 2008;190:5699-5709]. Physiological-molecular characterization of newly generated unmarked in-frame deletion and complementation mutants allowed defining ChnA (renamed here as Hped) as the enzyme responsible for 1-(4-hydroxyphenyl)-ethanol oxidation. Hped [1-(4-hydroxyphenyl)-ethanol dehydrogenase] belongs to the 'classical' family within the short-chain alcohol dehydrogenase/reductase (SDR) superfamily. Hped was overproduced in Escherichia coli, purified and crystallized. The X-ray structures of the apo- and NAD(+)-soaked form were resolved at 1.5 and 1.1 Å, respectively, and revealed Hped as a typical homotetrameric SDR. Modeling of the substrate 4-hydroxyacetophenone (reductive direction of Hped) into the active site revealed the structural determinants of the strict (R)-specificity of Hped (Phe(187)), contrasting the (S)-specificity of previously reported 1-phenylethanol dehydrogenase (Ped; Tyr(93)) from strain EbN1 [Höffken et al: Biochemistry 2006;45:82-93].
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Affiliation(s)
- Imke Büsing
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
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53
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Mutti FG, Knaus T, Scrutton NS, Breuer M, Turner NJ. Conversion of alcohols to enantiopure amines through dual-enzyme hydrogen-borrowing cascades. Science 2015; 349:1525-9. [PMID: 26404833 DOI: 10.1126/science.aac9283] [Citation(s) in RCA: 261] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
α-Chiral amines are key intermediates for the synthesis of a plethora of chemical compounds at industrial scale. We present a biocatalytic hydrogen-borrowing amination of primary and secondary alcohols that allows for the efficient and environmentally benign production of enantiopure amines. The method relies on a combination of two enzymes: an alcohol dehydrogenase (from Aromatoleum sp., Lactobacillus sp., or Bacillus sp.) operating in tandem with an amine dehydrogenase (engineered from Bacillus sp.) to aminate a structurally diverse range of aromatic and aliphatic alcohols, yielding up to 96% conversion and 99% enantiomeric excess. Primary alcohols were aminated with high conversion (up to 99%). This redox self-sufficient cascade possesses high atom efficiency, sourcing nitrogen from ammonium and generating water as the sole by-product.
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Affiliation(s)
- Francesco G Mutti
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, Manchester M1 7DN, UK. Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK.
| | - Tanja Knaus
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Michael Breuer
- BASF SE, White Biotechnology Research, GBW/B-A030, 67056 Ludwigshafen, Germany
| | - Nicholas J Turner
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, Manchester M1 7DN, UK.
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54
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Osuna S, Jiménez-Osés G, Noey EL, Houk KN. Molecular dynamics explorations of active site structure in designed and evolved enzymes. Acc Chem Res 2015; 48:1080-9. [PMID: 25738880 DOI: 10.1021/ar500452q] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP, a noncatalytic arrangement of the catalytic triad is dominant. Unnatural truncated substrates are inactive because of the lack of protein-protein interactions provided by the ACP. Directed evolution is able to gradually restore the catalytic organization of the active site by motion of the protein backbone that alters the active site geometry. In the third case, we demonstrate the key role of MD in combination with crystallography to identify the origins of substrate-dependent stereoselectivities in a number of Codexis-engineered ketoreductases, one of which is used commercially for the production of the antibiotic sulopenem. Here, mutations alter the shape of the active site as well as the accessibility of water to different regions of it. Each of these examples reveals something different about how mutations can influence enzyme activity and shows that directed evolution, like natural evolution, can increase catalytic activity in a variety of remarkable and often subtle ways.
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Affiliation(s)
- Sílvia Osuna
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, Campus Montilivi s/n, 17071 Girona, Spain
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Gonzalo Jiménez-Osés
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Elizabeth L. Noey
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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55
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Chen X, Liu ZQ, Huang JF, Lin CP, Zheng YG. Asymmetric synthesis of optically active methyl-2-benzamido-methyl-3-hydroxy-butyrate by robust short-chain alcohol dehydrogenases from Burkholderia gladioli. Chem Commun (Camb) 2015; 51:12328-31. [DOI: 10.1039/c5cc04652a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Specific short-chain alcohol dehydrogenases were discovered and used in the dynamic kinetic asymmetric transformation of methyl 2-benzamido-methyl-3-oxobutanoate with excellent stereo-selectivity.
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Affiliation(s)
- Xiang Chen
- Institute of Bioengineering, Zhejiang University of Technology
- Hangzhou 310014
- China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education
- Zhejiang University of Technology
| | - Zhi-Qiang Liu
- Institute of Bioengineering, Zhejiang University of Technology
- Hangzhou 310014
- China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education
- Zhejiang University of Technology
| | - Jian-Feng Huang
- Institute of Bioengineering, Zhejiang University of Technology
- Hangzhou 310014
- China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education
- Zhejiang University of Technology
| | - Chao-Ping Lin
- Institute of Bioengineering, Zhejiang University of Technology
- Hangzhou 310014
- China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education
- Zhejiang University of Technology
| | - Yu-Guo Zheng
- Institute of Bioengineering, Zhejiang University of Technology
- Hangzhou 310014
- China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education
- Zhejiang University of Technology
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56
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Sattler JH, Fuchs M, Mutti FG, Grischek B, Engel P, Pfeffer J, Woodley JM, Kroutil W. Introducing an in situ capping strategy in systems biocatalysis to access 6-aminohexanoic acid. Angew Chem Int Ed Engl 2014; 53:14153-7. [PMID: 25366462 DOI: 10.1002/anie.201409227] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 12/29/2022]
Abstract
The combination of two cofactor self-sufficient biocatalytic cascade modules allowed the successful transformation of cyclohexanol into the nylon-6 monomer 6-aminohexanoic acid at the expense of only oxygen and ammonia. A hitherto unprecedented carboxylic acid capping strategy was introduced to minimize the formation of the dead-end intermediate 6-hydroxyhexanoic acid. For this purpose, the precursor ε-caprolactone was converted in aqueous medium in the presence of methanol into the corresponding methyl ester instead of the acid. Hence, it was shown for the first time that esterases--specifically horse liver esterase--can perform the selective ring-opening of ε-caprolactone with a clear preference for methanol over water as the nucleophile.
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Affiliation(s)
- Johann H Sattler
- Institut für Chemie, Organische und Bioorganische Chemie, University of Graz, Heinrichstrasse 28, 8010 Graz (Austria); Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz (Austria)
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57
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Sattler JH, Fuchs M, Mutti FG, Grischek B, Engel P, Pfeffer J, Woodley JM, Kroutil W. Introducing an In Situ Capping Strategy in Systems Biocatalysis To Access 6-Aminohexanoic acid. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409227] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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58
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Whole-cell biotransformation systems for reduction of prochiral carbonyl compounds to chiral alcohol in Escherichia coli. Sci Rep 2014; 4:6750. [PMID: 25342633 PMCID: PMC4208033 DOI: 10.1038/srep06750] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
Lactobacillus brevis alcohol dehydrogenase (Lb-ADH) catalyzes reduction of prochiral carbonyl compounds to chiral alcohol and meanwhile consumes its cofactor NADH into NAD+, while the cofactor regeneration can be catalyzed by Candida boidinii formate dehydrogenase (Cb-FDH). This work presents three different Escherichia coli whole-cell biocatalyst systems expressing recombinant ADH/FDH, FDH-LIN1-ADH and FDH-LIN2-ADH, respectively, all of which display very high efficacies of prochiral carbonyl conversion with respect to conversion rates and enantiomeric excess values. ADH/FDH represents co-expression of Lb-ADH and Cb-FDH under different promoters in a single vector. Fusion of Lb-ADH and Cb-FDH by a linker peptide LIN1 (GGGGS)2 or LIN2 (EAAAK)2 generates the two bifunctional enzymes FDH-LIN1-ADH and FDH-LIN2-ADH, which enable efficient asymmetric reduction of prochiral ketones in whole-cell biotransformation.
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59
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Tang TX, Liu Y, Wu ZL. Characterization of a robust anti-Prelog short-chain dehydrogenase/reductase ChKRED20 from Chryseobacterium sp. CA49. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.03.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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60
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Liu Y, Tang TX, Pei XQ, Zhang C, Wu ZL. Identification of ketone reductase ChKRED20 from the genome of Chryseobacterium sp. CA49 for highly efficient anti-Prelog reduction of 3,5-bis(trifluoromethyl)acetophenone. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.01.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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61
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Rodríguez C, Borzęcka W, Sattler JH, Kroutil W, Lavandera I, Gotor V. Steric vs. electronic effects in the Lactobacillus brevis ADH-catalyzed bioreduction of ketones. Org Biomol Chem 2014; 12:673-81. [DOI: 10.1039/c3ob42057d] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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62
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Leuchs S, Lima-Ramos J, Greiner L, Al-Haque N, Tufvesson P, Woodley JM. Reaction Engineering of Biocatalytic Enantioselective Reduction: A Case Study for Aliphatic Ketones. Org Process Res Dev 2013. [DOI: 10.1021/op400117t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Joana Lima-Ramos
- Center for Process Engineering
and Technology, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Lasse Greiner
- Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, D-68163
Mannheim, Germany
| | - Naweed Al-Haque
- Center for Process Engineering
and Technology, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Pär Tufvesson
- Center for Process Engineering
and Technology, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - John M. Woodley
- Center for Process Engineering
and Technology, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
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63
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Leuchs S, Nonnen T, Dechambre D, Na’amnieh S, Greiner L. Continuous biphasic enzymatic reduction of aliphatic ketones. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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64
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Kulig J, Frese A, Kroutil W, Pohl M, Rother D. Biochemical characterization of an alcohol dehydrogenase from Ralstonia sp. Biotechnol Bioeng 2013; 110:1838-48. [PMID: 23381774 DOI: 10.1002/bit.24857] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 12/21/2012] [Accepted: 01/22/2013] [Indexed: 11/09/2022]
Abstract
Stereoselective reduction towards pharmaceutically potent products with multi-chiral centers is an ongoing hot topic, but up to now catalysts for reductions of bulky aromatic substrates are rare. The NADPH-dependent alcohol dehydrogenase from Ralstonia sp. (RADH) is an exception as it prefers sterically demanding substrates. Recent studies with this enzyme indicated outstanding potential for the reduction of various alpha-hydroxy ketones, but were performed with crude cell extract, which hampered its detailed characterization. We have established a procedure for the purification and storage of RADH and found a significantly stabilizing effect by addition of CaCl(2). Detailed analysis of the pH-dependent activity and stability yielded a broad pH-optimum (pH 6-9.5) for the reduction reaction and a sharp optimum of pH 10-11.5 for the oxidation reaction. The enzyme exhibits highest stability at pH 5.5-8 and 8-15°C; nevertheless, biotransformations can also be carried out at 25°C (half-life 80 h). Under optimized reaction parameters a thorough study of the substrate range of RADH including the reduction of different aldehydes and ketones and the oxidation of a broad range of alcohols was conducted. In contrast to most other known alcohol dehydrogenases, RADH clearly prefers aromatic and cyclic aliphatic compounds, which makes this enzyme unique for conversion of space demanding substrates. Further, reductions are catalyzed with extremely high stereoselectivity (>99% enantio- and diastereomeric excess). In order to identify appropriate substrate and cofactor concentrations for biotransformations, kinetic parameters were determined for NADP(H) and selected substrates. Among these, we studied the reduction of both enantiomers of 2-hydroxypropiophenone in more detail.
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Affiliation(s)
- Justyna Kulig
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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65
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Mayoral JG, Leonard KT, Nouzova M, Noriega FG, Defelipe LA, Turjanski AG. Functional analysis of a mosquito short-chain dehydrogenase cluster. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2013; 82:96-115. [PMID: 23238893 PMCID: PMC3697000 DOI: 10.1002/arch.21078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The short-chain dehydrogenases (SDR) constitute one of the oldest and largest families of enzymes with over 46,000 members in sequence databases. About 25% of all known dehydrogenases belong to the SDR family. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, hormone, and xenobiotic metabolism as well as in redox sensor mechanisms. This family is present in archaea, bacteria, and eukaryota, emphasizing their versatility and fundamental importance for metabolic processes. We identified a cluster of eight SDRs in the mosquito Aedes aegypti (AaSDRs). Members of the cluster differ in tissue specificity and developmental expression. Heterologous expression produced recombinant proteins that had diverse substrate specificities, but distinct from the conventional insect alcohol (ethanol) dehydrogenases. They are all NADP⁺-dependent and they have S-enantioselectivity and preference for secondary alcohols with 8-15 carbons. Homology modeling was used to build the structure of AaSDR1 and two additional cluster members. The computational study helped explain the selectivity toward the (10S)-isomers as well as the reduced activity of AaSDR4 and AaSDR9 for longer isoprenoid substrates. Similar clusters of SDRs are present in other species of insects, suggesting similar selection mechanisms causing duplication and diversification of this family of enzymes.
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Affiliation(s)
- Jaime G Mayoral
- Department of Biological Sciences, Florida International University, Miami, Florida, USA
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66
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Pennacchio A, Sannino V, Sorrentino G, Rossi M, Raia CA, Esposito L. Biochemical and structural characterization of recombinant short-chain NAD(H)-dependent dehydrogenase/reductase from Sulfolobus acidocaldarius highly enantioselective on diaryl diketone benzil. Appl Microbiol Biotechnol 2012; 97:3949-64. [DOI: 10.1007/s00253-012-4273-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
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67
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Naik HG, Yeniad B, Koning CE, Heise A. Investigation of asymmetric alcohol dehydrogenase (ADH) reduction of acetophenone derivatives: effect of charge density. Org Biomol Chem 2012; 10:4961-7. [DOI: 10.1039/c2ob06870b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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68
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Rocha-Martín J, Vega D, Bolivar JM, Hidalgo A, Berenguer J, Guisán JM, López-Gallego F. Characterization and further stabilization of a new anti-prelog specific alcohol dehydrogenase from Thermus thermophilus HB27 for asymmetric reduction of carbonyl compounds. BIORESOURCE TECHNOLOGY 2012; 103:343-350. [PMID: 22055107 DOI: 10.1016/j.biortech.2011.10.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/04/2011] [Accepted: 10/06/2011] [Indexed: 05/31/2023]
Abstract
The use of dehydrogenases in asymmetric chemistry has exponentially grown in the last decades facilitated by the genome mining. Here, a new short-chain alcohol dehydrogenase from Thermus thermophilus HB27 has been expressed, purified, characterized and stabilized by immobilization on solid supports. The enzyme catalyzes both oxidative and reductive reactions at neutral pH with a broad range of substrates. Its highest activity was found towards the reduction of 2,2',2″-trifluoroacetophenone (85 U/mg at 65 °C and pH 7). Moreover, the enzyme was stabilized more than 200-fold by multipoint covalent immobilization on agarose matrixes via glyoxyl chemistry. Such heterogeneous catalyst coupled to an immobilized cofactor recycling partner performed the quantitative asymmetric reduction of 2,2',2″-trifluoroacetophenone and rac-2-phenylpropanal to (S)-(+)-α-(trifluoromethyl)benzyl alcohol and (R)-2-phenyl-1-propanol with enantiomeric excesses of 96% and 71%, respectively. To our knowledge this is the first alcohol dehydrogenase from a thermophilic source with anti-Prelog selectivity for aryl ketones and that preferentially produces R-profens.
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Affiliation(s)
- Javier Rocha-Martín
- Departamento de Biocatálisis, Instituto de Catálisis y Petroleoquímica-CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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69
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Nie Y, Xiao R, Xu Y, Montelione GT. Novel anti-Prelog stereospecific carbonyl reductases from Candida parapsilosis for asymmetric reduction of prochiral ketones. Org Biomol Chem 2011; 9:4070-8. [PMID: 21505708 DOI: 10.1039/c0ob00938e] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of biocatalysis to the synthesis of chiral molecules is one of the greenest technologies for the replacement of chemical routes due to its environmentally benign reaction conditions and unparalleled chemo-, regio- and stereoselectivities. We have been interested in searching for carbonyl reductase enzymes and assessing their substrate specificity and stereoselectivity. We now report a gene cluster identified in Candida parapsilosis that consists of four open reading frames including three putative stereospecific carbonyl reductases (scr1, scr2, and scr3) and an alcohol dehydrogenase (cpadh). These newly identified three stereospecific carbonyl reductases (SCRs) showed high catalytic activities for producing (S)-1-phenyl-1,2-ethanediol from 2-hydroxyacetophenone with NADPH as the coenzyme. Together with CPADH, all four enzymes from this cluster are carbonyl reductases with novel anti-Prelog stereoselectivity. SCR1 and SCR3 exhibited distinct specificities to acetophenone derivatives and chloro-substituted 2-hydroxyacetophenones, and especially very high activities towards ethyl 4-chloro-3-oxobutyrate, a β-ketoester with important pharmaceutical potential. Our study also showed that genomic mining is a powerful tool for the discovery of new enzymes.
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Affiliation(s)
- Yao Nie
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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70
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Kulishova L, Dimoula K, Jordan M, Wirtz A, Hofmann D, Santiago-Schübel B, Fitter J, Pohl M, Spiess AC. Factors influencing the operational stability of NADPH-dependent alcohol dehydrogenase and an NADH-dependent variant thereof in gas/solid reactors. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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71
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Kale AJ, McGlinchey RP, Moore BS. Characterization of 5-chloro-5-deoxy-D-ribose 1-dehydrogenase in chloroethylmalonyl coenzyme A biosynthesis: substrate and reaction profiling. J Biol Chem 2010; 285:33710-7. [PMID: 20736169 PMCID: PMC2962469 DOI: 10.1074/jbc.m110.153833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 08/10/2010] [Indexed: 11/06/2022] Open
Abstract
SalM is a short-chain dehydrogenase/reductase enzyme from the marine actinomycete Salinispora tropica that is involved in the biosynthesis of chloroethylmalonyl-CoA, a novel halogenated polyketide synthase extender unit of the proteasome inhibitor salinosporamide A. SalM was heterologously overexpressed in Escherichia coli and characterized in vitro for its substrate specificity, kinetics, and reaction profile. A sensitive real-time (13)C NMR assay was developed to visualize the oxidation of 5-chloro-5-deoxy-D-ribose to 5-chloro-5-deoxy-D-ribono-γ-lactone in an NAD(+)-dependent reaction, followed by spontaneous lactone hydrolysis to 5-chloro-5-deoxy-D-ribonate. Although short-chain dehydrogenase/reductase enzymes are widely regarded as metal-independent, a strong divalent metal cation dependence for Mg(2+), Ca(2+), or Mn(2+) was observed with SalM. Oxidative activity was also measured with the alternative substrates D-erythrose and D-ribose, making SalM the first reported stereospecific non-phosphorylative ribose 1-dehydrogenase.
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Affiliation(s)
- Andrew J. Kale
- From the Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and
| | - Ryan P. McGlinchey
- From the Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and
| | - Bradley S. Moore
- From the Center of Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California 92093
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72
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Carius Y, Christian H, Faust A, Zander U, Klink BU, Kornberger P, Kohring GW, Giffhorn F, Scheidig AJ. Structural insight into substrate differentiation of the sugar-metabolizing enzyme galactitol dehydrogenase from Rhodobacter sphaeroides D. J Biol Chem 2010; 285:20006-14. [PMID: 20410293 PMCID: PMC2888412 DOI: 10.1074/jbc.m110.113738] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 04/07/2010] [Indexed: 01/29/2023] Open
Abstract
Galactitol 2-dehydrogenase (GatDH) belongs to the protein superfamily of short-chain dehydrogenases. As an enzyme capable of the stereo- and regioselective modification of carbohydrates, it exhibits a high potential for application in biotechnology as a biocatalyst. We have determined the crystal structure of the binary form of GatDH in complex with its cofactor NAD(H) and of the ternary form in complex with NAD(H) and three different substrates. The active form of GatDH constitutes a homo-tetramer with two magnesium-ion binding sites each formed by two opposing C termini. The catalytic tetrad is formed by Asn(116), Ser(144), Tyr(159), and Lys(163). GatDH structurally aligns well with related members of the short-chain dehydrogenase family. The substrate binding pocket can be divided into two parts of different size and polarity. In the smaller part, the side chains of amino acids Ser(144), Ser(146), and Asn(151) are important determinants for the binding specificity and the orientation of (pro-) chiral compounds. The larger part of the pocket is elongated and flanked by polar and non-polar residues, enabling a rather broad substrate spectrum. The presented structures provide valuable information for a rational design of this enzyme to improve its stability against pH, temperature, or solvent concentration and to optimize product yield in bioreactors.
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Affiliation(s)
- Yvonne Carius
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, Am Botanischen Garten 1–9, D-24118 Kiel
- the Department of Biophysics, Structural Biology, Saarland University, D-66421 Homburg, Germany
| | - Henning Christian
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, Am Botanischen Garten 1–9, D-24118 Kiel
- the Institute for Microbiology and Genetics, Department for Molecular Structural Biology, Georg-August-University of Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, and
| | - Annette Faust
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, Am Botanischen Garten 1–9, D-24118 Kiel
| | - Ulrich Zander
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, Am Botanischen Garten 1–9, D-24118 Kiel
- the Department of Biophysics, Structural Biology, Saarland University, D-66421 Homburg, Germany
| | - Björn U. Klink
- the Division of Structural Biology, Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig
- the Department of Biophysics, Structural Biology, Saarland University, D-66421 Homburg, Germany
| | - Petra Kornberger
- the Institute for Applied Microbiology, Saarland University, Im Stadtwald, D-66123 Saarbrücken
| | - Gert-Wieland Kohring
- the Institute for Applied Microbiology, Saarland University, Im Stadtwald, D-66123 Saarbrücken
| | - Friedrich Giffhorn
- the Institute for Applied Microbiology, Saarland University, Im Stadtwald, D-66123 Saarbrücken
| | - Axel J. Scheidig
- From the Department of Structural Biology, Zoological Institute, Christian-Albrechts-University Kiel, Am Botanischen Garten 1–9, D-24118 Kiel
- the Department of Biophysics, Structural Biology, Saarland University, D-66421 Homburg, Germany
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73
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Biochemical characterization of a recombinant short-chain NAD(H)-dependent dehydrogenase/reductase from Sulfolobus acidocaldarius. Extremophiles 2010; 14:193-204. [PMID: 20049620 DOI: 10.1007/s00792-009-0298-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 12/16/2009] [Indexed: 10/20/2022]
Abstract
The gene encoding a novel alcohol dehydrogenase that belongs to the short-chain dehydrogenases/reductases (SDRs) superfamily was identified in the aerobic thermoacidophilic crenarchaeon Sulfolobus acidocaldarius strain DSM 639. The saadh gene was heterologously overexpressed in Escherichia coli, and the protein (SaADH) was purified to homogeneity and characterized. SaADH is a tetrameric enzyme consisting of identical 28,978-Da subunits, each composed of 264 amino acids. The enzyme has remarkable thermophilicity and thermal stability, displaying activity at temperatures up to 75 degrees C and a 30-min half-inactivation temperature of ~90 degrees C, and shows good tolerance to common organic solvents. SaADH has a strict requirement for NAD(H) as the coenzyme, and displays a preference for the reduction of alicyclic, bicyclic and aromatic ketones and alpha-keto esters, but is poorly active on aliphatic, cyclic and aromatic alcohols, and shows no activity on aldehydes. The enzyme catalyses the reduction of alpha-methyl and alpha-ethyl benzoylformate, and methyl o-chlorobenzoylformate with 100% conversion to methyl (S)-mandelate [17% enantiomeric excess (ee)], ethyl (R)-mandelate (50% ee), and methyl (R)-o-chloromandelate (72% ee), respectively, with an efficient in situ NADH-recycling system which involves glucose and a thermophilic glucose dehydrogenase. This study provides further evidence supporting the critical role of the D37 residue in discriminating NAD(H) from NAD(P)H in members of the SDR superfamily.
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74
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Weckbecker A, Gröger H, Hummel W. Regeneration of nicotinamide coenzymes: principles and applications for the synthesis of chiral compounds. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 120:195-242. [PMID: 20182929 DOI: 10.1007/10_2009_55] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dehydrogenases which depend on nicotinamide coenzymes are of increasing interest for the preparation of chiral compounds, either by reduction of a prochiral precursor or by oxidative resolution of their racemate. The regeneration of oxidized and reduced nicotinamide cofactors is a very crucial step because the use of these cofactors in stoichiometric amounts is too expensive for application. There are several possibilities to regenerate nicotinamide cofactors: established methods such as formate/formate dehydrogenase (FDH) for the regeneration of NADH, recently developed electrochemical methods based on new mediator structures, or the application of gene cloning methods for the construction of "designed" cells by heterologous expression of appropriate genes.A very promising approach is enzymatic cofactor regeneration. Only a few enzymes are suitable for the regeneration of oxidized nicotinamide cofactors. Glutamate dehydrogenase can be used for the oxidation of NADH as well as NADPH while L: -lactate dehydrogenase is able to oxidize NADH only. The reduction of NAD(+) is carried out by formate and FDH. Glucose-6-phosphate dehydrogenase and glucose dehydrogenase are able to reduce both NAD(+) and NADP(+). Alcohol dehydrogenases (ADHs) are either NAD(+)- or NADP(+)-specific. ADH from horse liver, for example, reduces NAD(+) while ADHs from Lactobacillus strains catalyze the reduction of NADP(+). These enzymes can be applied by their inclusion in whole cell biotransformations with an NAD(P)(+)-dependent primary reaction to achieve in situ the regeneration of the consumed cofactor.Another efficient method for the regeneration of nicotinamide cofactors is the electrochemical approach. Cofactors can be regenerated directly, for example at a carbon anode, or indirectly involving mediators such as redox catalysts based on transition-metal complexes.An increasing number of examples in technical scale applications are known where nicotinamide dependent enzymes were used together with cofactor regenerating enzymes.
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Affiliation(s)
- Andrea Weckbecker
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University of Düsseldorf, Research Centre Jülich, Stetternicher Forst, 52426, Jülich, Germany
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75
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Cacchi S, Cirilli R, Fabrizi G, Sgalla S, Macone A, Bonamore A, Boffi A. (R)-1-Arylethanols from aryl iodides through a two-step one-pot enantioselective chemoenzymatic process. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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76
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Xiao ZJ, Zong MH, Lou WY. Highly enantioselective reduction of 4-(trimethylsilyl)-3-butyn-2-one to enantiopure (R)-4-(trimethylsilyl)-3-butyn-2-ol using a novel strain Acetobacter sp. CCTCC M209061. BIORESOURCE TECHNOLOGY 2009; 100:5560-5565. [PMID: 19564106 DOI: 10.1016/j.biortech.2009.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 05/31/2009] [Accepted: 06/02/2009] [Indexed: 05/28/2023]
Abstract
The biocatalytic reduction of 4-(trimethylsilyl)-3-butyn-2-one to enantiopure (R)-4-(trimethylsilyl)-3-butyn-2-ol was successfully conducted with high enantioselectivity using immobilized whole cells of a novel strain Acetobacter sp. CCTCC M209061, newly isolated from kefir. Compared with other microorganisms that were investigated, Acetobacter sp. CCTCC M209061 was shown to be more effective for the bioreduction reaction, and afforded much higher yield and product enantiomeric excess (e.e.). The optimal buffer pH, co-substrate concentration, reaction temperature, substrate concentration and shaking rate were 5.0, 130.6 mM, 30 degrees C, 6.0 mM and 180 r/min, respectively. Under the optimized conditions, the maximum yield and the product e.e. were 71% and >99%, respectively, which are much higher than those reported previously. Additionally, the established biocatalytic system proved to be efficient for the bioreduction of acetyltrimethylsilane to (R)-1-trimethylsilylethanol with excellent yield and product e.e. The immobilized cells manifested a good operational stability under the above reaction conditions since they retained 70% of their catalytic activity after ten cycles of use.
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Affiliation(s)
- Zi-Jun Xiao
- State Key Laboratory of Pulp and Paper Engineering, College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
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77
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Expression, purification and characterization of recombinant protein tyrosine phosphatase from Thermus thermophilus HB27. Acta Biochim Biophys Sin (Shanghai) 2009; 41:689-98. [DOI: 10.1093/abbs/gmp057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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78
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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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79
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New Model for Polymerization of Oligomeric Alcohol Dehydrogenases into Nanoaggregates. Appl Biochem Biotechnol 2009; 160:1188-205. [DOI: 10.1007/s12010-009-8646-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 04/12/2009] [Indexed: 10/20/2022]
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80
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Schrittwieser JH, Lavandera I, Seisser B, Mautner B, Kroutil W. Biocatalytic Cascade for the Synthesis of Enantiopure β-Azidoalcohols and β-Hydroxynitriles. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900091] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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81
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Caseli L, Perinotto AC, Viitala T, Zucolotto V, Oliveira ON. Immobilization of alcohol dehydrogenase in phospholipid Langmuir-Blodgett films to detect ethanol. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3057-3061. [PMID: 19437773 DOI: 10.1021/la8037445] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Enzyme immobilization in nanostructured films may be useful for a number of biomimetic systems, particularly if suitable matrixes are identified. Here we show that alcohol dehydrogenase (ADH) has high affinity toward a negatively charged phospholipid, dimyristoylphosphatidic acid (DMPA), which forms a Langmuir monolayer at an air-water interface. Incorporation of ADH into the DMPA monolayer was monitored with surface pressure measurements and polarization-modulation infrared reflection absorption spectroscopy, with the alpha-helices from ADH being mainly oriented parallel to the water surface. ADH remained at the interface even at high surface pressures, thus allowing deposition of Langmuir-Blodgett (LB) films from the DMPA-ADH film. Indeed, interaction with DMPA enhances the transfer of ADH, where the mass transferred onto a solid support increased from 134 ng for ADH on a Gibbs monolayer to 178 ng for an LB film with DMPA. With fluorescence spectroscopy it was possible to confirm that the ADH structure was preserved even after one month of the LB deposition. ADH-containing films deposited onto gold-interdigitated electrodes were employed in a sensor array capable of detecting ethanol at concentrations down to 10 ppb (in volume), using impedance spectroscopy as the method of detection.
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Affiliation(s)
- Luciano Caseli
- Departamento de Ciências Exatas e da Terra, Universidade Federal de São Paulo, Diadema, Brazil.
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82
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Machielsen R, Looger LL, Raedts J, Dijkhuizen S, Hummel W, Hennemann HG, Daussmann T, van der Oost J. Cofactor engineering ofLactobacillus brevisalcohol dehydrogenase by computational design. Eng Life Sci 2009. [DOI: 10.1002/elsc.200800046] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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83
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Wiemann LO, Buthe A, Klein M, van den Wittenboer A, Dähne L, Ansorge-Schumacher MB. Encapsulation of synthetically valuable biocatalysts into polyelectrolyte multilayer systems. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:618-623. [PMID: 19209447 DOI: 10.1021/la803152c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Layer-by-Layer (LbL) technology recently turned out to be a versatile tool for the encapsulation of bioactive entities. In this study, the factual potential of this technology to encapsulate synthetically valuable biocatalysts, that is enzymes and whole cells expressing a specific catalytic activity, was investigated. The biocatalysts were embedded into a polyelectrolyte multilayer system involving poly(allylamine) hydrochloride (PAH) and poly(styrene sulfonate) sodium salt (PSS). The enzymes were adsorbed to CaCO3 or DEAE-cellulose previous to encapsulation. A slight increase (32%) of the catalytic performance was observed for lipase B from Candida antarctica when four layers of polyelectrolytes were applied. On the whole, however, the residual activity of the investigated enzymes after encapsulation was rather low. Similar results were obtained with whole-cell biocatalysts. It was found that the activity decrease can be attributed to mass transfer restrictions as well as direct interactions between polyelectrolytes and catalytically active molecules. Both effects need to be understood in more detail before LbL technology can be advanced to technically efficient biocatalysis.
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Affiliation(s)
- Lars O Wiemann
- RWTH Aachen UniVersity, Department of Biotechnology, Worringerweg 1, D-52074 Aachen, Germany
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84
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Ng JF, Jaenicke S. Immobilized Whole Cells as Effective Catalysts for Chiral Alcohol Production. Aust J Chem 2009. [DOI: 10.1071/ch09112] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recombinant Escherichia coli overexpressing the gene LbADH, which encodes for an alcohol dehydrogenase from Lactobacillus brevis, was successfully transformed and cultured. The cells are able to catalyze the reduction of pro-chiral ketones, e.g. ethyl acetoacetate into R-(–)ethyl hydroxybutyrate (EHB) with high conversion and enantiomeric excess >99%. Immobilizing the whole cells in alginate beads leads to a catalyst with improved stability and ease of handling while maintaining the high activity of the free cells. The whole-cell catalyst was tested in a stirred batch reactor (CSTR) and in a continuously operated packed-bed reactor. An Mg2+ concentration of 2 mM was crucial for maintaining the activity of the biocatalyst. After a partial optimization of the process conditions, a productivity of 1.4 gEHB gwcw–1 h–1 could be maintained in a continuous flow reactor over a prolonged period of time.
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85
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Kwiecień RA, Ayadi F, Nemmaoui Y, Silvestre V, Zhang BL, Robins RJ. Probing stereoselectivity and pro-chirality of hydride transfer during short-chain alcohol dehydrogenase activity: a combined quantitative 2H NMR and computational approach. Arch Biochem Biophys 2008; 482:42-51. [PMID: 19061855 DOI: 10.1016/j.abb.2008.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 11/04/2008] [Accepted: 11/08/2008] [Indexed: 10/21/2022]
Abstract
Different members of the alcohol oxidoreductase family can transfer the hydride of NAD(P)H to either the re- or the si-face of the substrate. The enantioselectivity of transfer is very variable, even for a range of substrates reduced by the same enzyme. Exploiting quantitative isotopic (2)H NMR to measure the transfer of (2)H from NAD(P)(2)H to ethanol, a range of enantiomeric excess between 0.38 and 0.98, depending on the origin of the enzyme and the nature of the cofactor, has been determined. Critically, in no case was only (R)-[1-(2)H]ethanol or (S)-[1-(2)H]ethanol obtained. By calculating the relative energies of the active site models for hydride transfer to the re- or si-face of short-chain aldehydes by alcohol dehydrogenase from Saccharomyces cerevisiae and Lactobacillus brevis, it is shown that the differences in the energy of the systems when the substrate is positioned with the alkyl group in one or the other pocket of the active site could play a role in determining stereoselectivity. These experiments help to provide insight into structural features that influence the potential catalytic flexibility of different alcohol dehydrogenase activities.
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Affiliation(s)
- Renata A Kwiecień
- Unit for Interdisciplinary Chemistry: Synthesis, Analysis, Modeling, UMR CNRS6230, CNRS, University of Nantes, 2 rue de la Houssinière, Nantes, France
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86
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Purification and characterization of a novel recombinant highly enantioselective short-chain NAD(H)-dependent alcohol dehydrogenase from Thermus thermophilus. Appl Environ Microbiol 2008; 74:3949-58. [PMID: 18456852 DOI: 10.1128/aem.00217-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene encoding a novel alcohol dehydrogenase (ADH) that belongs to the short-chain dehydrogenase/reductase (SDR) superfamily was identified in the extremely thermophilic, halotolerant gram-negative eubacterium Thermus thermophilus HB27. The T. thermophilus ADH gene (adh(Tt)) was heterologously overexpressed in Escherichia coli, and the protein (ADH(Tt)) was purified to homogeneity and characterized. ADH(Tt) is a tetrameric enzyme consisting of identical 26,961-Da subunits composed of 256 amino acids. The enzyme has remarkable thermophilicity and thermal stability, displaying activity at temperatures up to approximately 73 degrees C and a 30-min half-inactivation temperature of approximately 90 degrees C, as well as good tolerance to common organic solvents. ADH(Tt) has a strict requirement for NAD(H) as the coenzyme, a preference for reduction of aromatic ketones and alpha-keto esters, and poor activity on aromatic alcohols and aldehydes. This thermophilic enzyme catalyzes the following reactions with Prelog specificity: the reduction of acetophenone, 2,2,2-trifluoroacetophenone, alpha-tetralone, and alpha-methyl and alpha-ethyl benzoylformates to (S)-(-)-1-phenylethanol (>99% enantiomeric excess [ee]), (R)-alpha-(trifluoromethyl)benzyl alcohol (93% ee), (S)-alpha-tetralol (>99% ee), methyl (R)-(-)-mandelate (92% ee), and ethyl (R)-(-)-mandelate (95% ee), respectively, by way of an efficient in situ NADH-recycling system involving 2-propanol and a second thermophilic ADH. This study further supports the critical role of the D37 residue in discriminating NAD(H) from NADP(H) in members of the SDR superfamily.
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87
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Nie Y, Xu Y, Mu XQ, Wang HY, Yang M, Xiao R. Purification, characterization, gene cloning, and expression of a novel alcohol dehydrogenase with anti-prelog stereospecificity from Candida parapsilosis. Appl Environ Microbiol 2007; 73:3759-64. [PMID: 17435004 PMCID: PMC1932682 DOI: 10.1128/aem.02185-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2006] [Accepted: 03/31/2007] [Indexed: 11/20/2022] Open
Abstract
An alcohol dehydrogenase from Candida parapsilosis CCTCC M203011 was characterized along with its biochemical activity and structural gene. The amino acid sequence shows similarity to those of the short-chain dehydrogenase/reductases but no overall identity to known proteins. This enzyme with unusual stereospecificity catalyzes an anti-Prelog reduction of 2-hydroxyacetophenone to (S)-1-phenyl-1,2-ethanediol.
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Affiliation(s)
- Yao Nie
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Southern Yangtze University, Wuxi 214122, People's Republic of China
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88
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Chong PK, Burja AM, Radianingtyas H, Fazeli A, Wright PC. Translational and transcriptional analysis of Sulfolobus solfataricus P2 to provide insights into alcohol and ketone utilisation. Proteomics 2007; 7:424-35. [PMID: 17211831 DOI: 10.1002/pmic.200600746] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The potential of Sulfolobus solfataricus P2 for alcohol or ketone bioconversion was explored in this study. S. solfataricus was grown in different concentrations (0.1-0.8% w/v) of alcohols or ketones (ethanol, iso-propanol, n-propanol, acetone, phenol and hexanol) in the presence of 0.4% w/v glucose. Consequently, the addition of these alcohols or ketones into the growth media had an inhibitory effect on biomass production, whereby lag times increased and specific growth rates decreased when compared to a glucose control. Complete glucose utilisation was observed in all cultures, although slower rates of glucose consumption were observed in experimental cultures (average of 14.9 mg/L/h compared to 18.9 mg/L/h in the control). On the other hand, incomplete solvent utilisation was observed, with the highest solvent consumption being approximately 51% of the initial concentration in acetone cultures. Translational responses of S. solfataricus towards these alcohols or ketones were then investigated using the isobaric tags for relative and absolute quantitation (iTRAQ) technique. The majority (>80%) of proteins identified and quantified showed no discernable changes in regulation compared to the control. These results, along with those obtained from transcriptional analysis of key genes involved within this catabolic process using quantitative RT-PCR and metabolite analysis, demonstrate successful alcohol or ketone conversion in S. solfataricus.
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Affiliation(s)
- Poh Kuan Chong
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, University of Sheffield, Sheffield, UK
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89
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90
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Vermeulen N, Czerny M, Gänzle MG, Schieberle P, Vogel RF. Reduction of (E)-2-nonenal and (E,E)-2,4-decadienal during sourdough fermentation. J Cereal Sci 2007. [DOI: 10.1016/j.jcs.2006.07.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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91
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Gänzle MG, Vermeulen N, Vogel RF. Carbohydrate, peptide and lipid metabolism of lactic acid bacteria in sourdough. Food Microbiol 2006; 24:128-38. [PMID: 17008155 DOI: 10.1016/j.fm.2006.07.006] [Citation(s) in RCA: 239] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The metabolic pathways of lactic acid bacteria that influence bread quality are coupled to the central carbon flux by the availability of cofactors influencing the cellular and environmental redox potential. Homo- and heterofermentative metabolism differ fundamentally with respect to the requirement for regeneration of reduced cofactors, NADH or NADPH. The utilization of co-substrates such as oxygen or fructose as electron acceptors by obligate heterofermentative lactobacilli is coupled to an increased production of acetate in dough. Recently, several oxidoreductases involved in cofactor regeneration were characterized and glutathione and short-chain aldehydes derived from lipid oxidation were identified as substrates for cofactor regeneration by Lactobacillus sanfranciscensis. Based on the different metabolic requirements for cofactor regeneration, homo- and heterofermentative lactobacilli exert divergent effects on redox-reactions in sourdough that influence bread quality beyond the formation of acetate. Proteolysis, followed by peptide or amino acid metabolism by LAB is one of the key routes of flavour formation in bread flavour, and enables the strain-specific formation of antifungal metabolites. Peptide metabolism as well as the metabolism of cysteine, arginine, and phenylalanine in Lactobacillus plantarum, L. sanfranciscensis, and Lactobacillus pontis is increasingly understood and these insights provide new opportunities for the directed application of sourdough LAB for improved bread quality.
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Affiliation(s)
- Michael G Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Ag/For Centre, Edmonton, Alta., Canada T6G 2P5.
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92
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Kung CCS, Huang WN, Huang YC, Yeh KC. Proteomic survey of copper-binding proteins inArabidopsis roots by immobilized metal affinity chromatography and mass spectrometry. Proteomics 2006; 6:2746-58. [PMID: 16526091 DOI: 10.1002/pmic.200500108] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To plants, copper is vitally essential at low concentrations but extremely toxic at elevated concentrations. Plants have evolved a suite of mechanisms that modulate the uptake, distribution, and utilization of copper ions. These mechanisms require copper-interacting proteins for transporting, chelating, and sequestrating copper ions. In this study, we have systematically screened for copper-interacting proteins in Arabidopsis roots via copper-immobilized metal affinity chromatography (Cu-IMAC). We also compared Arabidopsis root metalloproteomes with affinity to Cu-IMAC and Zn-IMAC. From the identities of 38 protein spots with affinity to Cu-IMAC, 35 unique proteins were identified. Functional classification of these proteins includes redox/hydrolytic reactions, amino acid metabolism, glutathione metabolism, phosphorylation, translation machinery, membrane-associated proteins, and vegetative storage proteins. Potential copper-interacting motifs were predicted and scored. Six candidate motifs, H-(X)5 -H, H-(X)7 -H, H-(X)12 -H, H-(X)6 -M, M-(X)7 -H, and H-(X)3 -C, are present in Cu-IMAC-isolated proteins with higher frequency than in the whole Arabidopsis proteome.
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Affiliation(s)
- Cheng-Che S Kung
- Institute of BioAgricultural Sciences, Academia Sinica, Taipei, Taiwan, Republic of China
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93
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Höffken HW, Duong M, Friedrich T, Breuer M, Hauer B, Reinhardt R, Rabus R, Heider J. Crystal structure and enzyme kinetics of the (S)-specific 1-phenylethanol dehydrogenase of the denitrifying bacterium strain EbN1. Biochemistry 2006; 45:82-93. [PMID: 16388583 DOI: 10.1021/bi051596b] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(S)-1-Phenylethanol dehydrogenase (PED) from the denitrifying bacterium strain EbN1 catalyzes the NAD+-dependent, stereospecific oxidation of (S)-1-phenylethanol to acetophenone and the biotechnologically interesting reverse reaction. This novel enzyme belongs to the short-chain alcohol dehydrogenase/aldehyde reductase family. The coding gene (ped) was heterologously expressed in Escherichia coli and the purified protein was crystallized. The X-ray structures of the apo-form and the NAD+-bound form were solved at a resolution of 2.1 and 2.4 A, respectively, revealing that the enzyme is a tetramer with two types of hydrophobic dimerization interfaces, similar to beta-oxoacyl-[acyl carrier protein] reductase (FabG) from E. coli. NAD+-binding is associated with a conformational shift of the substrate binding loop of PED from a crystallographically unordered "open" to a more ordered "closed" form. Modeling the substrate acetophenone into the active site revealed the structural prerequisites for the strong enantioselectivity of the enzyme and for the catalytic mechanism. Studies on the steady-state kinetics of PED indicated a highly positive cooperativity of both catalytic directions with respect to the substrates. This is contrasted by the behavior of FabG. Moreover, PED exhibits extensive regulation on the enzyme level, being inhibited by elevated concentrations of substrates and products, as well as the wrong enantiomer of 1-phenylethanol. These regulatory properties of PED are consistent with the presence of a putative "transmission module" between the subunits. This module consists of the C-terminal loops of all four subunits, which form a special interconnected structural domain and mediate close contact of the subunits, and of a phenylalanine residue in each subunit that reaches out between substrate-binding loop and C-terminal domain of an adjacent subunit. These elements may transmit the substrate-induced conformational change of the substrate binding loop from one subunit to the others in the tetrameric complex and thus mediate the cooperative behavior of PED.
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Affiliation(s)
- H Wolfgang Höffken
- BASF AG, Physical Chemistry and Informatics, 67056 Ludwigshafen, Germany.
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94
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95
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Hirakawa H, Kamiya N, Kawarabayashi Y, Nagamune T. Properties of an alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix K1. J Biosci Bioeng 2005; 97:202-6. [PMID: 16233615 DOI: 10.1016/s1389-1723(04)70191-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Accepted: 12/26/2003] [Indexed: 11/30/2022]
Abstract
A NAD+-dependent medium-chain alcohol dehydrogenase from the hyperthermophilic archaeon Aeropyrum pernix K1 was expressed in Escherichia coli and purified. The recombinant enzyme was a homotetramer of molecular mass 1.6 x 10(2) kDa. The optimum pH for the oxidative reaction was around 10.5 and that for the reductive reaction was around 8.0. The enzyme had a broad substrate specificity including aliphatic and aromatic alcohols, aliphatic and aromatic ketones, and benzylaldehyde. This enzyme produced (S)-alcohols from the corresponding ketones. The enzyme was thermophilic and the catalytic activity increased up to 95 degrees C. It maintained 24% of the original catalytic activity after incubation for 30 min at 98 degrees C, indicating that this enzyme is highly thermostable.
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Affiliation(s)
- Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
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96
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Kumarevel T, Mizuno H, Kumar PKR. Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis. Nucleic Acids Res 2005; 33:5494-502. [PMID: 16192572 PMCID: PMC1236978 DOI: 10.1093/nar/gki868] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
HutP is an RNA-binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis, by binding to cis-acting regulatory sequences on hut mRNA. It requires L-histidine and an Mg2+ ion for binding to the specific sequence within the hut mRNA. In the present study, we show that several divalent cations can mediate the HutP–RNA interactions. The best divalent cations were Mn2+, Zn2+ and Cd2+, followed by Mg2+, Co2+ and Ni2+, while Cu2+, Yb2+ and Hg2+ were ineffective. In the HutP–RNA interactions, divalent cations cannot be replaced by monovalent cations, suggesting that a divalent metal ion is required for mediating the protein–RNA interactions. To clarify their importance, we have crystallized HutP in the presence of three different metal ions (Mg2+, Mn2+ and Ba2+), which revealed the importance of the metal ion binding site. Furthermore, these analyses clearly demonstrated how the metal ions cause the structural rearrangements that are required for the hut mRNA recognition.
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Affiliation(s)
| | - Hiroshi Mizuno
- NEC Soft Ltd1-18-6, Shinkiba, Koto-ku, Tokyo 106-8608, Japan
| | - Penmetcha K. R. Kumar
- To whom correspondence should be addressed. Tel: +81 298 61 6085; Fax: +81 298 61 6095;
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97
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Schlieben NH, Niefind K, Müller J, Riebel B, Hummel W, Schomburg D. Atomic Resolution Structures of R-specific Alcohol Dehydrogenase from Lactobacillus brevis Provide the Structural Bases of its Substrate and Cosubstrate Specificity. J Mol Biol 2005; 349:801-13. [PMID: 15896805 DOI: 10.1016/j.jmb.2005.04.029] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 04/08/2005] [Accepted: 04/14/2005] [Indexed: 11/15/2022]
Abstract
The R-specific alcohol dehydrogenase (RADH) from Lactobacillus brevis is an NADP-dependent, homotetrameric member of the extended enzyme family of short-chain dehydrogenases/reductases (SDR) with a high biotechnological application potential. Its preferred in vitro substrates are prochiral ketones like acetophenone with almost invariably a small methyl group as one substituent and a bulky (often aromatic) moiety as the other. On the basis of an atomic-resolution structure of wild-type RADH in complex with NADP and acetophenone, we designed the mutant RADH-G37D, which should possess an improved cosubstrate specificity profile for biotechnological purposes, namely, a preference for NAD rather than NADP. Comparative kinetic measurements with wild-type and mutant RADH showed that this aim was achieved. To characterize the successful mutant structurally, we determined several, partly atomic-resolution, crystal structures of RADH-G37D both as an apo-enzyme and as ternary complex with NAD or NADH and phenylethanol. The increased affinity of RADH-G37D for NAD(H) depends on an interaction between the adenosine ribose moiety of NAD and the inserted aspartate side-chain. A structural comparison between RADH-G37D as apo-enzyme and as a part of a ternary complex revealed significant rearrangements of Ser141, Glu144, Tyr189 and Met205 in the vicinity of the active site. This plasticity contributes to generate a small hydrophobic pocket for the methyl group typical for RADH substrates, and a hydrophobic coat for the second, more variable and often aromatic, substituent. Around Ser141 we even found alternative conformations in the backbone. A structural adaptability in this region, which we describe here for the first time for an SDR enzyme, is probably functionally important, because it concerns Ser142, a member of the highly conserved catalytic tetrad typical for SDR enzymes. Moreover, it affects an extended proton relay system that has been identified recently as a critical element for the catalytic mechanism in SDR enzymes.
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Affiliation(s)
- Nils Helge Schlieben
- Universität zu Köln, Institut für Biochemie, Zülpicher Strasse 47, D-50674 Köln, Germany
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98
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Ernst M, Kaup B, Müller M, Bringer-Meyer S, Sahm H. Enantioselective reduction of carbonyl compounds by whole-cell biotransformation, combining a formate dehydrogenase and a (R)-specific alcohol dehydrogenase. Appl Microbiol Biotechnol 2004; 66:629-34. [PMID: 15549291 DOI: 10.1007/s00253-004-1765-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Accepted: 08/31/2004] [Indexed: 10/26/2022]
Abstract
A whole-cell biotransformation system for the reduction of prochiral carbonyl compounds, such as methyl acetoacetate, to chiral hydroxy acid derivatives [methyl (R)-3-hydroxy butanoate] was developed in Escherichia coli by construction of a recombinant oxidation/reduction cycle. Alcohol dehydrogenase from Lactobacillus brevis catalyzes a highly regioselective and enantioselective reduction of several ketones or keto acid derivatives to chiral alcohols or hydroxy acid esters. The adh gene encoding for the alcohol dehydrogenase of L. brevis was expressed in E. coli. As expected, whole cells of the recombinant strain produced only low quantities of methyl (R)-3-hydroxy butanoate from the substrate methyl acetoacetate. Therefore, the fdh gene from Mycobacterium vaccae N10, encoding NAD+-dependent formate dehydrogenase, was functionally coexpressed. The resulting two-fold recombinant strain exhibited an in vitro catalytic alcohol dehydrogenase activity of 6.5 units mg-1 protein in reducing methyl acetoacetate to methyl (R)-3-hydroxy butanoate with NADPH as the cofactor and 0.7 units mg-1 protein with NADH. The in vitro formate dehydrogenase activity was 1.3 units mg-1 protein. Whole resting cells of this strain catalyzed the formation of 40 mM methyl (R)-3-hydroxy butanoate from methyl acetoacetate. The product yield was 100 mol% at a productivity of 200 micromol g-1 (cell dry weight) min-1. In the presence of formate, the intracellular [NADH]/[NAD+] ratio of the cells increased seven-fold. Thus, the functional overexpression of alcohol dehydrogenase in the presence of formate dehydrogenase was sufficient to enable and sustain the desired reduction reaction via the relatively low specific activity of alcohol dehydrogenase with NADH, instead of NADPH, as a cofactor.
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Affiliation(s)
- Marianne Ernst
- Institut für Biotechnologie 1, Forschungszentrum Jülich GmbH, 52425, Julich, Germany
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99
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Kroutil W, Mang H, Edegger K, Faber K. Recent advances in the biocatalytic reduction of ketones and oxidation of sec -alcohols. Curr Opin Chem Biol 2004; 8:120-6. [PMID: 15062771 DOI: 10.1016/j.cbpa.2004.02.005] [Citation(s) in RCA: 299] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To improve the efficiency and applicability of biocatalytic redox-reactions for asymmetric ketone-reduction and enantioselective alcohol-oxidation catalyzed by nicotinamide-dependent dehydrogenases/reductases, several achievements for cofactor-recycling have been made during the last two years. First, the use of hydrogenases for NADPH recycling in a two enzyme system. Second, preparative transformations with alcohol dehydrogenases coupled with NADH oxidases for NAD+/NADP+ recycling. Third, an exceptional chemo-stable alcohol dehydrogenase can efficiently use i-propanol and acetone as cosubstrates for reduction and oxidation, respectively, in a single-enzyme system. Novel carbonyl reductases and dehydrogenases derived from plant cells are particularly suited for sterically demanding substrates.
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Affiliation(s)
- Wolfgang Kroutil
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Graz, Austria
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100
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Homann MJ, Vail RB, Previte E, Tamarez M, Morgan B, Dodds DR, Zaks A. Rapid identification of enantioselective ketone reductions using targeted microbial libraries. Tetrahedron 2004. [DOI: 10.1016/j.tet.2003.10.123] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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