1
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Mukhopadhyay A, Karu K, Dalby PA. Two-substrate enzyme engineering using small libraries that combine the substrate preferences from two different variant lineages. Sci Rep 2024; 14:1287. [PMID: 38218974 PMCID: PMC10787763 DOI: 10.1038/s41598-024-51831-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
Improving the range of substrates accepted by enzymes with high catalytic activity remains an important goal for the industrialisation of biocatalysis. Many enzymes catalyse two-substrate reactions which increases the complexity in engineering them for the synthesis of alternative products. Often mutations are found independently that can improve the acceptance of alternatives to each of the two substrates. Ideally, we would be able to combine mutations identified for each of the two alternative substrates, and so reprogramme new enzyme variants that synthesise specific products from their respective two-substrate combinations. However, as we have previously observed for E. coli transketolase, the mutations that improved activity towards aromatic acceptor aldehydes, did not successfully recombine with mutations that switched the donor substrate to pyruvate. This likely results from several active site residues having multiple roles that can affect both of the substrates, as well as structural interactions between the mutations themselves. Here, we have designed small libraries, including both natural and non-natural amino acids, based on the previous mutational sites that impact on acceptance of the two substrates, to achieve up to 630× increases in kcat for the reaction with 3-formylbenzoic acid (3-FBA) and pyruvate. Computational docking was able to determine how the mutations shaped the active site to improve the proximity of the 3-FBA substrate relative to the enamine-TPP intermediate, formed after the initial reaction with pyruvate. This work opens the way for small libraries to rapidly reprogramme enzyme active sites in a plug and play approach to catalyse new combinations of two-substrate reactions.
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Affiliation(s)
- Arka Mukhopadhyay
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK
| | - Kersti Karu
- Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, UCL, Bernard Katz Building, Gower Street, London, WC1E 6BT, UK.
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2
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Liang Y, Zhao J, Yang Y, Hung SF, Li J, Zhang S, Zhao Y, Zhang A, Wang C, Appadoo D, Zhang L, Geng Z, Li F, Zeng J. Stabilizing copper sites in coordination polymers toward efficient electrochemical C-C coupling. Nat Commun 2023; 14:474. [PMID: 36710270 PMCID: PMC9884666 DOI: 10.1038/s41467-023-35993-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Electroreduction of carbon dioxide with renewable electricity holds promise for achieving net-zero carbon emissions. Single-site catalysts have been reported to catalyze carbon-carbon (C-C) coupling-the indispensable step for more valuable multi-carbon (C2+) products-but were proven to be transformed in situ to metallic agglomerations under working conditions. Here, we report a stable single-site copper coordination polymer (Cu(OH)BTA) with periodic neighboring coppers and it exhibits 1.5 times increase of C2H4 selectivity compared to its metallic counterpart at 500 mA cm-2. In-situ/operando X-ray absorption, Raman, and infrared spectroscopies reveal that the catalyst remains structurally stable and does not undergo a dynamic transformation during reaction. Electrochemical and kinetic isotope effect analyses together with computational calculations show that neighboring Cu in the polymer provides suitably-distanced dual sites that enable the energetically favorable formation of an *OCCHO intermediate post a rate-determining step of CO hydrogenation. Accommodation of this intermediate imposes little changes of conformational energy to the catalyst structure during the C-C coupling. We stably operate full-device CO2 electrolysis at an industry-relevant current of one ampere for 67 h in a membrane electrode assembly. The coordination polymers provide a perspective on designing molecularly stable, single-site catalysts for electrochemical CO2 conversion.
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Affiliation(s)
- Yongxiang Liang
- grid.59053.3a0000000121679639Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 P. R. China
| | - Jiankang Zhao
- grid.59053.3a0000000121679639Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 P. R. China
| | - Yu Yang
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering and The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006 Australia
| | - Sung-Fu Hung
- grid.260539.b0000 0001 2059 7017Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 300 Taiwan
| | - Jun Li
- grid.16821.3c0000 0004 0368 8293Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shuzhen Zhang
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering and The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006 Australia
| | - Yong Zhao
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering and The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006 Australia
| | - An Zhang
- grid.59053.3a0000000121679639Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 P. R. China
| | - Cheng Wang
- grid.59053.3a0000000121679639Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 P. R. China
| | - Dominique Appadoo
- grid.248753.f0000 0004 0562 0567Australian Synchrotron, Clayton, VIC 3168 Australia
| | - Lei Zhang
- grid.59053.3a0000000121679639Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 P. R. China
| | - Zhigang Geng
- grid.59053.3a0000000121679639Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 P. R. China
| | - Fengwang Li
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering and The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006 Australia
| | - Jie Zeng
- grid.59053.3a0000000121679639Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 P. R. China
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3
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Li A, Cai L, Chen Z, Wang M, Wang N, Nakanishi H, Gao XD, Li Z. Recent advances in the synthesis of rare sugars using DHAP-dependent aldolases. Carbohydr Res 2017; 452:108-115. [PMID: 29096183 DOI: 10.1016/j.carres.2017.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/04/2017] [Accepted: 10/17/2017] [Indexed: 01/02/2023]
Abstract
The occurrence rates of non-communicable diseases like obesity, diabetes and hyperlipidemia have increased remarkably due to excessive consumption of a high-energy diet. Rare sugars therefore have become increasingly attractive owing to their unique nutritional properties. In the past two decades, various rare sugars have been successfully prepared guided by the "Izumoring strategy". As a valuable complement to the Izumoring approach, the controllable dihydroxyacetone phosphate (DHAP)-dependent aldolases have generally predictable regio- and stereoselectivity, which makes them powerful tools in C-C bond construction and rare sugar production. However, the main disadvantage for this group of aldolases is their strict substrate specificity toward the donor molecule DHAP, a very expensive and relatively unstable compound. Among the current methods involving DHAP, the one that couples DHAP production from inexpensive starting materials (for instance, glycerol, DL-glycerol 3-phosphate, dihydroxyacetone, and glucose) with aldol condensation appears to be the most promising. This review thus focuses on recent advances in the application of L-rhamnulose-1-phosphate aldolase (RhaD), L-fuculose-1-phosphate aldolase (FucA), and D-fructose-1,6-bisphosphate aldolase (FruA) for rare sugar synthesis in vitro and in vivo, while illustrating strategies for supplying DHAP in efficient and economical ways.
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Affiliation(s)
- Aimin Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Li Cai
- Department of Chemistry, University of South Carolina Lancaster, 476 Hubbard Drive, Lancaster, SC, 29720, USA
| | - Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Mayan Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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4
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Affaticati PE, Dai SB, Payongsri P, Hailes HC, Tittmann K, Dalby PA. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes. Sci Rep 2016; 6:35716. [PMID: 27767080 PMCID: PMC5073344 DOI: 10.1038/srep35716] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022] Open
Abstract
The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies.
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Affiliation(s)
- Pierre E Affaticati
- Department of Biochemical Engineering, Gordon Street, University College London, WC1H 0AH, UK
| | - Shao-Bo Dai
- Albrecht-von-Haller Institute, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Panwajee Payongsri
- Department of Biochemical Engineering, Gordon Street, University College London, WC1H 0AH, UK
| | - Helen C Hailes
- Department of Chemistry, 20 Gordon Street, University College London, WC1H 0AJ, UK
| | - Kai Tittmann
- Albrecht-von-Haller Institute, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Paul A Dalby
- Department of Biochemical Engineering, Gordon Street, University College London, WC1H 0AH, UK
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5
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Affiliation(s)
- Liuqing Wen
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kenneth Huang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yunpeng Liu
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National
Glycoengineering Research Center, Shandong University, Jinan 250100, China
| | - Peng George Wang
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- National
Glycoengineering Research Center, Shandong University, Jinan 250100, China
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6
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Hajipour AR, Khorsandi Z, Farrokhpour H. Regioselective Heck reaction catalyzed by Pd nanoparticles immobilized on DNA-modified MWCNTs. RSC Adv 2016. [DOI: 10.1039/c6ra11737f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This is the first report of regioselective Heck reaction of aryl iodides with 2,3-dihydrofuran using heterogonous nanocatalyst.
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Affiliation(s)
- Abdol R. Hajipour
- Pharmaceutical Research Laboratory
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- Iran
| | - Zahra Khorsandi
- Pharmaceutical Research Laboratory
- Department of Chemistry
- Isfahan University of Technology
- Isfahan
- Iran
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7
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Li Z, He B, Gao Y, Cai L. Synthesis of D-Sorbose and D-Psicose by RecombinantEscherichia coli. J Carbohydr Chem 2015. [DOI: 10.1080/07328303.2015.1068794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Payongsri P, Steadman D, Hailes HC, Dalby PA. Second generation engineering of transketolase for polar aromatic aldehyde substrates. Enzyme Microb Technol 2015; 71:45-52. [DOI: 10.1016/j.enzmictec.2015.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 10/24/2022]
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9
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Characterization of glycerol phosphate oxidase from Streptococcus pneumoniae and its application for ketose synthesis. Bioorg Med Chem Lett 2015; 25:504-7. [DOI: 10.1016/j.bmcl.2014.12.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 11/20/2022]
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10
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11
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Hammer SC, Dominicus JM, Syrén PO, Nestl BM, Hauer B. Stereoselective Friedel–Crafts alkylation catalyzed by squalene hopene cyclases. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Li Z, Cai L, Wei M, Wang PG. One-pot four-enzyme synthesis of ketoses with fructose 1,6-bisphosphate aldolases from Staphylococcus carnosus and rabbit muscle. Carbohydr Res 2012; 357:143-6. [PMID: 22727596 DOI: 10.1016/j.carres.2012.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/04/2012] [Accepted: 05/07/2012] [Indexed: 10/28/2022]
Abstract
By the action of D-fructose 1,6-bisphosphate aldolases (FruA) from rabbit muscle and Staphylococcus carnosus, various ketoses were synthesized from glyceraldehydes or other aliphatic aldehydes as acceptors in a one-pot four-enzyme system.
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Affiliation(s)
- Zijie Li
- National Glycoengineering Research Center, The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
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13
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Milner SE, Moody TS, Maguire AR. Biocatalytic Approaches to the Henry (Nitroaldol) Reaction. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101840] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Li Z, Cai L, Qi Q, Wang PG. Enzymatic synthesis of D-sorbose and D-psicose with aldolase RhaD: effect of acceptor configuration on enzyme stereoselectivity. Bioorg Med Chem Lett 2011; 21:7081-4. [PMID: 22018788 PMCID: PMC3210396 DOI: 10.1016/j.bmcl.2011.09.087] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 09/19/2011] [Accepted: 09/21/2011] [Indexed: 11/28/2022]
Abstract
It was previously reported that DHAP-dependent aldolase RhaD selectively chooses L-glyceraldehyde from racemic glyceraldehyde to produce l-fructose exclusively. Contrastingly, we discovered that D-glyceraldehyde is also tolerated as an acceptor and the stereoselectivity of the enzyme is lost in the corresponding aldol addition. Furthermore, we applied this property to efficiently synthesize two rare sugars D-sorbose and D-psicose.
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Affiliation(s)
- Zijie Li
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
- National Glycoengineering Research Center and The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, PR China
| | - Li Cai
- University of South Carolina Salkehatchie, Walterboro, SC 29488, USA
| | - Qingsheng Qi
- National Glycoengineering Research Center and The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, PR China
| | - Peng George Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA
- National Glycoengineering Research Center and The State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, PR China
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15
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Li Z, Cai L, Qi Q, Styslinger TJ, Zhao G, Wang PG. Synthesis of rare sugars with L-fuculose-1-phosphate aldolase (FucA) from Thermus thermophilus HB8. Bioorg Med Chem Lett 2011; 21:5084-7. [PMID: 21482110 PMCID: PMC3445428 DOI: 10.1016/j.bmcl.2011.03.072] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 03/15/2011] [Accepted: 03/17/2011] [Indexed: 11/20/2022]
Abstract
We report herein a one-pot four-enzyme approach for the synthesis of the rare sugars d-psicose, d-sorbose, l-tagatose, and l-fructose with aldolase FucA from a thermophilic source (Thermus thermophilus HB8). Importantly, the cheap starting material DL-GP (DL-glycerol 3-phosphate), was used to significantly reduce the synthetic cost.
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Affiliation(s)
- Zijie Li
- National Glycoengineering Research Center and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Li Cai
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Qingsheng Qi
- National Glycoengineering Research Center and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Thomas J. Styslinger
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Guohui Zhao
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Peng George Wang
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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16
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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17
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Schmidt M, Böttcher D, Bornscheuer UT. Directed Evolution of Industrial Biocatalysts. Ind Biotechnol (New Rochelle N Y) 2010. [DOI: 10.1002/9783527630233.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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18
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Protein engineering of microbial enzymes. Curr Opin Microbiol 2010; 13:274-82. [PMID: 20171138 DOI: 10.1016/j.mib.2010.01.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 01/14/2010] [Accepted: 01/15/2010] [Indexed: 11/20/2022]
Abstract
Protein engineering has emerged as an important tool to overcome the limitations of natural enzymes as biocatalysts. Recent advances have mainly focused on applying directed evolution to enzymes, especially important for organic synthesis, such as monooxygenases, ketoreductases, lipases or aldolases in order to improve their activity, enantioselectivity, and stability. The combination of directed evolution and rational protein design using computational tools is becoming increasingly important in order to explore enzyme sequence-space and to create improved or novel enzymes. These developments should allow to further expand the application of microbial enzymes in industry.
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19
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Fronza G, Fuganti C, Serra S. Stereochemical Course of Baker's Yeast Mediated Reduction of the Tri- and Tetrasubstituted Double Bonds of Substituted Cinnamaldehydes. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900827] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Stecher H, Tengg M, Ueberbacher B, Remler P, Schwab H, Griengl H, Gruber-Khadjawi M. Biocatalytic Friedel-Crafts Alkylation Using Non-natural Cofactors. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200905095] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Stecher H, Tengg M, Ueberbacher B, Remler P, Schwab H, Griengl H, Gruber-Khadjawi M. Biocatalytic Friedel-Crafts Alkylation Using Non-natural Cofactors. Angew Chem Int Ed Engl 2009; 48:9546-8. [DOI: 10.1002/anie.200905095] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Fryszkowska A, Toogood H, Sakuma M, Gardiner JM, Stephens GM, Scrutton NS. Asymmetric Reduction of Activated Alkenes by Pentaerythritol Tetranitrate Reductase: Specificity and Control of Stereochemical Outcome by Reaction Optimisation. Adv Synth Catal 2009; 351:2976-2990. [PMID: 20396613 PMCID: PMC2854813 DOI: 10.1002/adsc.200900603] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We show that pentaerythritol tetranitrate reductase (PETNR), a member of the 'ene' reductase old yellow enzyme family, catalyses the asymmetric reduction of a variety of industrially relevant activated alpha,beta-unsaturated alkenes including enones, enals, maleimides and nitroalkenes. We have rationalised the broad substrate specificity and stereochemical outcome of these reductions by reference to molecular models of enzyme-substrate complexes based on the crystal complex of the PETNR with 2-cyclohexenone 4a. The optical purity of products is variable (49-99% ee), depending on the substrate type and nature of substituents. Generally, high enantioselectivity was observed for reaction products with stereogenic centres at Cbeta (>99% ee). However, for the substrates existing in two isomeric forms (e.g., citral 11a or nitroalkenes 18-19a), an enantiodivergent course of the reduction of E/Z-forms may lead to lower enantiopurities of the products. We also demonstrate that the poor optical purity obtained for products with stereogenic centres at Calpha is due to non-enzymatic racemisation. In reactions with ketoisophorone 3a we show that product racemisation is prevented through reaction optimisation, specifically by shortening reaction time and through control of solution pH. We suggest this as a general strategy for improved recovery of optically pure products with other biocatalytic conversions where there is potential for product racemisation.
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Affiliation(s)
- Anna Fryszkowska
- Manchester Interdisciplinary Biocentre, The School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Helen Toogood
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Michiyo Sakuma
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - John M. Gardiner
- Manchester Interdisciplinary Biocentre, The School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Gill M. Stephens
- Manchester Interdisciplinary Biocentre, The School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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23
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Linder M, Brinck T. Synergistic activation of the Diels-Alder reaction by an organic catalyst and substituents: a computational study. Org Biomol Chem 2009; 7:1304-11. [PMID: 19300814 DOI: 10.1039/b818655c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theory (DFT), using the hybrid functionals B3LYP and B2PLYP, has been employed to investigate the activation of the acrolein-butadiene Diels-Alder reaction, mediated by a thiourea catalyst. Effects due to electron-donating groups (EDGs) on the diene, as well as electron-withdrawing groups (EWGs) on the dienophile, have also been studied. Organic catalysts such as thioureas are known to lower the activation energy through hydrogen-bonding to the carbonyl oxygen, in a way that mimics the oxyanion holes of hydrolytic enzymes. EDGs and EWGs were found to further activate the reaction, and the catalyst showed a synergistic behavior towards the EDGs. Polar solvents were found to reduce the overall activation energy, but also the relative catalytic effect of the thiourea, in accordance with experimental studies. The substituent-mediated reactions displayed more asynchronous transition structures with lower activation energy, which led us to investigate the possibility of an alternative two-step, Michael-type route, similar to what has been found in macrophomate synthase. Although the concerted Diels-Alder route was found to be favored over the Michael route, the calculated activation energy difference is less than 1 kcal mol(-1), which suggests that the two mechanisms compete, and could be responsible for the particular stereochemical outcome of an experiment.
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Affiliation(s)
- Mats Linder
- Physical Chemistry, Royal Institute of Technology (KTH), Stockholm, Sweden
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24
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Shaeri J, Wright I, Rathbone EB, Wohlgemuth R, Woodley JM. Characterization of enzymatic D-xylulose 5-phosphate synthesis. Biotechnol Bioeng 2008; 101:761-7. [PMID: 18553501 DOI: 10.1002/bit.21949] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this article we report on the characterization of the enzymatic synthesis of D-xylulose 5-phosphate using triosephosphate isomerase and transketolase. Two potential starting substrates are possible with this scheme. The data presented here allow a comparison of both routes for the synthesis, based on experimental information on reaction kinetics. Operational guidelines are proposed which should assist in the scale-up of such syntheses.
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Affiliation(s)
- Jobin Shaeri
- Department of Biochemical Engineering, University College London, Torrington Place, London, UK
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25
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Separation of amino acids by simulated moving bed under solvent constrained conditions for the integration of continuous chromatography and biotransformation. Chem Eng Sci 2008. [DOI: 10.1016/j.ces.2008.07.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Kourtoglou E, Mamma D, Topakas E, Christakopoulos P. Purification, characterization and mass spectrometric sequencing of transaldolase from Fusarium oxysporum. Process Biochem 2008. [DOI: 10.1016/j.procbio.2008.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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van der Kamp MW, Perruccio F, Mulholland AJ. Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase. Proteins 2007; 69:521-35. [PMID: 17623847 DOI: 10.1002/prot.21482] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Citrate synthase is an archetypal carbon-carbon bond forming enzyme. It promotes the conversion of oxaloacetate (OAA) to citrate by catalyzing the deprotonation (enolization) of acetyl-CoA, followed by nucleophilic attack of the enolate form of this substrate on OAA to form a citryl-CoA intermediate and subsequent hydrolysis. OAA is strongly bound to the active site and its alpha-carbonyl group is polarized. This polarization has been demonstrated spectroscopically, [(Kurz et al., Biochemistry 1985;24:452-457; Kurz and Drysdale, Biochemistry 1987;26:2623-2627)] and has been suggested to be an important catalytic strategy. Substrate polarization is believed to be important in many enzymes. The first step, formation of the acetyl-CoA enolate intermediate, is thought to be rate-limiting in the mesophilic (pig/chicken) enzyme. We have examined the effects of substrate polarization on this key step using quantum mechanical/molecular mechanical (QM/MM) methods. Free energy profiles have been calculated by AM1/CHARMM27 umbrella sampling molecular dynamics (MD) simulations, together with potential energy profiles. To study the influence of OAA polarization, profiles were calculated with different polarization of the OAA alpha-carbonyl group. The results indicate that OAA polarization influences catalysis only marginally but has a larger effect on intermediate stabilization. Different levels of treatment of OAA are compared (MM or QM), and its polarization in the protein and in water analyzed at the B3LYP/6-31+G(d)/CHARMM27 level. Analysis of stabilization by individual residues shows that the enzyme mainly stabilizes the enolate intermediate (not the transition state) through electrostatic (including hydrogen bond) interactions: these contribute much more than polarization of OAA.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
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28
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Purkarthofer T, Skranc W, Schuster C, Griengl H. Potential and capabilities of hydroxynitrile lyases as biocatalysts in the chemical industry. Appl Microbiol Biotechnol 2007; 76:309-20. [PMID: 17607575 DOI: 10.1007/s00253-007-1025-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 05/02/2007] [Accepted: 05/21/2007] [Indexed: 11/29/2022]
Abstract
The application of hydroxynitrile lyases (HNLs) as catalysts for the stereoselective condensation of HCN with carbonyl compounds has been reported as early as 1908. This enzymatic C-C bond coupling reaction furnishes enantiopure cyanohydrins which serve as versatile bifunctional building blocks for chemical synthesis. Screening of natural sources led to the discovery of both (R)- and (S)-selective HNLs, and several distinctly different classes of these enzymes with substantial differences concerning sequence, structure, and mechanism have been found. Especially during the last two centuries, HNLs have been developed into valuable biocatalysts, which can be produced in recombinant form by overexpression in microbial hosts, resulting in the implementation of industrial processes utilizing these enzymes. Recently, protein engineering in combination with in silico methods gave rise to the development of a tailor-made HNL for large-scale manufacturing of a specific target cyanohydrin.
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29
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Makart S, Bechtold M, Panke S. Towards preparative asymmetric synthesis of β-hydroxy-α-amino acids: l-allo-Threonine formation from glycine and acetaldehyde using recombinant GlyA. J Biotechnol 2007; 130:402-10. [PMID: 17597243 DOI: 10.1016/j.jbiotec.2007.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 04/23/2007] [Accepted: 05/08/2007] [Indexed: 11/25/2022]
Abstract
The diastereospecific formation of L-allo-threonine, catalyzed by the serine hydroxymethyltransferase GlyA form Escherichia coli, was studied with regard to the application in continuous processes. Process design will rely on a suitable description of enzyme stability and kinetics under relevant process conditions. Therefore, the effects of addition of organic co-solvents--methanol and acetonitrile--to the reaction mixtures on activity, stability, and diastereoselectivity were investigated. A series of progress curves from batch reactions at 35 degrees C in 50mM sodium phosphate buffer pH 6.6 and 50mM sodium phosphate buffer pH 6.6 in 20% methanol was used to estimate the respective kinetic parameters for an appropriate kinetic model. The experimental data agreed well with a kinetic model for an ordered reaction mechanism of the type bi-uni including the formation of a ternary complex and a pseudo-equilibrium assumption. The model was then applied in order to simulate the performance of the enzyme in an enzyme membrane reactor (EMR) and gave an excellent agreement with the corresponding experimental data. A space time yield of 227g L(-1)d(-1) was achieved in a continuous running EMR without significant loss of enzyme activity over 120 h of operation.
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Affiliation(s)
- Stefan Makart
- Bioprocess Laboratory, Institute of Process Engineering, ETH Zurich, Universitätsstrasse 6, 8092 Zurich, Switzerland
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Gruber-Khadjawi M, Purkarthofer T, Skranc W, Griengl H. Hydroxynitrile Lyase-Catalyzed Enzymatic Nitroaldol (Henry) Reaction. Adv Synth Catal 2007. [DOI: 10.1002/adsc.200700064] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Hult K, Berglund P. Enzyme promiscuity: mechanism and applications. Trends Biotechnol 2007; 25:231-8. [PMID: 17379338 DOI: 10.1016/j.tibtech.2007.03.002] [Citation(s) in RCA: 424] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 02/12/2007] [Accepted: 03/08/2007] [Indexed: 10/23/2022]
Abstract
Introductory courses in biochemistry teach that enzymes are specific for their substrates and the reactions they catalyze. Enzymes diverging from this statement are sometimes called promiscuous. It has been suggested that relaxed substrate and reaction specificities can have an important role in enzyme evolution; however, enzyme promiscuity also has an applied aspect. Enzyme condition promiscuity has, for a long time, been used to run reactions under conditions of low water activity that favor ester synthesis instead of hydrolysis. Together with enzyme substrate promiscuity, it is exploited in numerous synthetic applications, from the laboratory to industrial scale. Furthermore, enzyme catalytic promiscuity, where enzymes catalyze accidental or induced new reactions, has begun to be recognized as a valuable research and synthesis tool. Exploiting enzyme catalytic promiscuity might lead to improvements in existing catalysts and provide novel synthesis pathways that are currently not available.
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Affiliation(s)
- Karl Hult
- School of Biotechnology, Department of Biochemistry, Royal Institute of Technology (KTH), AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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32
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Rogers PL, Jeon YJ, Lee KJ, Lawford HG. Zymomonas mobilis for fuel ethanol and higher value products. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 108:263-88. [PMID: 17522816 DOI: 10.1007/10_2007_060] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
High oil prices, increasing focus on renewable carbohydrate-based feedstocks for fuels and chemicals, and the recent publication of its genome sequence, have provided continuing stimulus for studies on Zymomonas mobilis. However, despite its apparent advantages of higher yields and faster specific rates when compared to yeasts, no commercial scale fermentations currently exist which use Z. mobilis for the manufacture of fuel ethanol. This may change with the recent announcement of a Dupont/Broin partnership to develop a process for conversion of lignocellulosic residues, such as corn stover, to fuel ethanol using recombinant strains of Z. mobilis. The research leading to the construction of these strains, and their fermentation characteristics, are described in the present review. The review also addresses opportunities offered by Z. mobilis for higher value products through its metabolic engineering and use of specific high activity enzymes.
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Affiliation(s)
- P L Rogers
- School of Biotechnology and Biomolecular Sciences, UNSW, 2052 Sydney, Australia.
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33
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Williams GJ, Woodhall T, Farnsworth LM, Nelson A, Berry A. Creation of a Pair of Stereochemically Complementary Biocatalysts. J Am Chem Soc 2006; 128:16238-47. [PMID: 17165777 DOI: 10.1021/ja065233q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-Acetylneuraminic acid lyase (NAL) exhibits poor facial selectivity during carbon-carbon formation, and as such, its utility as a catalyst for use in synthetic chemistry is limited. For example, the NAL-catalyzed condensation between pyruvate and (2R,3S)-2,3-dihydroxy-4-oxo-N,N-dipropylbutyramide yields ca. 3:1 mixtures of diastereomeric products under either kinetic or thermodynamic control. Engineering the stereochemical course of NAL-catalyzed reactions could remove this limitation. We used directed evolution to create a pair of stereochemically complementary variant NALs for the synthesis of sialic acid mimetics. The E192N variant, a highly efficient catalyst for aldol reactions of (2R,3S)-2,3-dihydroxy-4-oxo-N,N-dialkylbutyramides, was chosen as a starting point. Initially, error-prone PCR identified residues in the active site of NAL that contributed to the stereochemical control of an aldolase-catalyzed reaction. Subsequently, an intense structure-guided program of saturation and site-directed mutagenesis was used to identify a complementary pair of variants, E192N/T167G and E192N/T167V/S208V, which were approximately 50-fold selective toward the cleavage of the alternative 4S- and 4R-configured condensation products, respectively. It was shown that wild-type NAL could not be used for the highly stereoselective synthesis of a 6-dipropylamide sialic acid mimetic because the 4S-configured product was only approximately 3-fold kinetically favored and only approximately 3-fold thermodynamically favored over the alternative 4R-configured product. However, the complementary 4R- and 4S-selective variants allowed the highly (>98:<2) diastereoselective synthesis of both 4S- and 4R-configured products under kinetic control from the same starting materials. Conversion of an essentially nonselective aldolase into a pair of complementary biocatalysts will be of enormous interest to synthetic chemists. Furthermore, since residues identified as critical for stereoselectivity are conserved among members of the NAL superfamily, the approach might be extended to the evolution of other useful biocatalysts for the stereoselective synthesis of biologically active molecules.
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Affiliation(s)
- Gavin J Williams
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom
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Lee JH, Bae J, Kim D, Choi Y, Im YJ, Koh S, Kim JS, Kim MK, Kang GB, Hong SI, Lee DS, Eom SH. Stereoselectivity of fructose-1,6-bisphosphate aldolase in Thermus caldophilus. Biochem Biophys Res Commun 2006; 347:616-25. [PMID: 16843441 DOI: 10.1016/j.bbrc.2006.06.139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Accepted: 06/21/2006] [Indexed: 10/24/2022]
Abstract
It was recently established that fructose-1,6-bisphosphate (FBP) aldolase (FBA) and tagatose-1,6-bisphosphate (TBP) aldolase (TBA), two class II aldolases, are highly specific for the diastereoselective synthesis of FBP and TBP from glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP), respectively. In this paper, we report on a FBA from the thermophile Thermus caldophilus GK24 (Tca) that produces both FBP and TBP from C(3) substrates. Moreover, the FBP:TBP ratio could be adjusted by manipulating the concentrations of G3P and DHAP. This is the first native FBA known to show dual diastereoselectivity among the FBAs and TBAs characterized thus far. To explain the behavior of this enzyme, the X-ray crystal structure of the Tca FBA in complex with DHAP was determined at 2.2A resolution. It appears that as a result of alteration of five G3P binding residues, the substrate binding cavity of Tca FBA has a greater volume than those in the Escherichia coli FBA-phosphoglycolohydroxamate (PGH) and TBA-PGH complexes. We suggest that this steric difference underlies the difference in the diastereoselectivities of these class II aldolases.
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Affiliation(s)
- Jun Hyuck Lee
- Department of Life Science, Gwangju Institute of Science and Technology, Republic of Korea
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35
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Samland AK, Sprenger GA. Microbial aldolases as C-C bonding enzymes--unknown treasures and new developments. Appl Microbiol Biotechnol 2006; 71:253-64. [PMID: 16614860 DOI: 10.1007/s00253-006-0422-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/10/2006] [Accepted: 03/10/2006] [Indexed: 11/26/2022]
Abstract
Aldolases are a specific group of lyases that catalyze the reversible stereoselective addition of a donor compound (nucleophile) onto an acceptor compound (electrophile). Whereas most aldolases are specific for their donor compound in the aldolization reaction, they often tolerate a wide range of aldehydes as acceptor compounds. C-C bonding by aldolases creates stereocenters in the resulting aldol products. This makes aldolases interesting tools for asymmetric syntheses of rare sugars or sugar-derived compounds as iminocyclitols, statins, epothilones, and sialic acids. Besides the well-known fructose 1,6-bisphosphate aldolase, other aldolases of microbial origin have attracted the interest of synthetic bio-organic chemists in recent years. These are either other dihydroxyacetone phosphate aldolases or aldolases depending on pyruvate/phosphoenolpyruvate, glycine, or acetaldehyde as donor substrate. Recently, an aldolase that accepts dihydroxyacetone or hydroxyacetone as a donor was described. A further enlargement of the arsenal of available chemoenzymatic tools can be achieved through screening for novel aldolase activities and directed evolution of existing aldolases to alter their substrate- or stereospecifities. We give an update of work on aldolases, with an emphasis on microbial aldolases.
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Affiliation(s)
- Anne K Samland
- Institut für Mikrobiologie, Universität Stuttgart, Germany
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36
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Enzymatic resolution of 1,1-dimethoxybut-3-en-2-ol and 1,1-dimethoxypent-4-en-2-ol, α-hydroxyaldehyde precursors for aldol-type reactions. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2005.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Theodossis A, Walden H, Westwick EJ, Connaris H, Lamble HJ, Hough DW, Danson MJ, Taylor GL. The Structural Basis for Substrate Promiscuity in 2-Keto-3-deoxygluconate Aldolase from the Entner-Doudoroff Pathway in Sulfolobus solfataricus. J Biol Chem 2004; 279:43886-92. [PMID: 15265860 DOI: 10.1074/jbc.m407702200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hyperthermophilic Archaea Sulfolobus solfataricus grows optimally above 80 degrees C and metabolizes glucose by a non-phosphorylative variant of the Entner-Doudoroff pathway. In this pathway glucose dehydrogenase and gluconate dehydratase catalyze the oxidation of glucose to gluconate and the subsequent dehydration of gluconate to D-2-keto-3-deoxygluconate (KDG). KDG aldolase (KDGA) then catalyzes the cleavage of KDG to D-glyceraldehyde and pyruvate. It has recently been shown that all the enzymes of this pathway exhibit a catalytic promiscuity that also enables them to be used for the metabolism of galactose. This phenomenon, known as metabolic pathway promiscuity, depends crucially on the ability of KDGA to cleave KDG and D-2-keto-3-deoxygalactonate (KDGal), in both cases producing pyruvate and D-glyceraldehyde. In turn, the aldolase exhibits a remarkable lack of stereoselectivity in the condensation reaction of pyruvate and D-glyceraldehyde, forming a mixture of KDG and KDGal. We now report the structure of KDGA, determined by multiwavelength anomalous diffraction phasing, and confirm that it is a member of the tetrameric N-acetylneuraminate lyase superfamily of Schiff base-forming aldolases. Furthermore, by soaking crystals of the aldolase at more than 80 degrees C below its temperature activity optimum, we have been able to trap Schiff base complexes of the natural substrates pyruvate, KDG, KDGal, and pyruvate plus D-glyceraldehyde, which have allowed rationalization of the structural basis of promiscuous substrate recognition and catalysis. It is proposed that the active site of the enzyme is rigid to keep its thermostability but incorporates extra functionality to be promiscuous.
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Affiliation(s)
- Alex Theodossis
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, Fife KY16 9ST, Scotland
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38
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Demir AS, Ayhan P, Igdir A, Duygu A. Enzyme catalyzed hydroxymethylation of aromatic aldehydes with formaldehyde. Synthesis of hydroxyacetophenones and (S)-benzoins. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.06.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sánchez-Moreno I, García-García JF, Bastida A, García-Junceda E. Multienzyme system for dihydroxyacetone phosphate-dependent aldolase catalyzed C-C bond formation from dihydroxyacetone. Chem Commun (Camb) 2004:1634-5. [PMID: 15263954 DOI: 10.1039/b405220j] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A multienzyme system composed by recombinant dihydroxyacetone kinase from Citrobacter freundii, fuculose-1-phosphate aldolase and acetate kinase, allows a practical one-pot C-C bond formation catalysed by dihydroxyacetone phosphate-dependent aldolases from dihydroxyacetone and an aldehyde.
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Affiliation(s)
- Israel Sánchez-Moreno
- Departamento de Química Orgánica Biológica, Instituto de Química Orgánica General, CSIC, Madrid 28006, Spain
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40
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