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Lee SH, Yeom SJ, Kim SE, Oh DK. Development of aldolase-based catalysts for the synthesis of organic chemicals. Trends Biotechnol 2021; 40:306-319. [PMID: 34462144 DOI: 10.1016/j.tibtech.2021.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 11/28/2022]
Abstract
Aldol chemicals are synthesized by condensation reactions between the carbon units of ketones and aldehydes using aldolases. The efficient synthesis of diverse organic chemicals requires intrinsic modification of aldolases via engineering and design, as well as extrinsic modification through immobilization or combination with other catalysts. This review describes the development of aldolases, including their engineering and design, and the selection of desired aldolases using high-throughput screening, to enhance their catalytic properties and perform novel reactions. Aldolase-containing catalysts, which catalyze the aldol reaction combined with other enzymatic and/or chemical reactions, can efficiently synthesize diverse complex organic chemicals using inexpensive and simple materials as substrates. We also discuss the current challenges and emerging solutions for aldolase-based catalysts.
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Affiliation(s)
- Seon-Hwa Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
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2
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Warkentin R, Kwan DH. Resources and Methods for Engineering "Designer" Glycan-Binding Proteins. Molecules 2021; 26:E380. [PMID: 33450899 PMCID: PMC7828330 DOI: 10.3390/molecules26020380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/04/2021] [Accepted: 01/10/2021] [Indexed: 12/11/2022] Open
Abstract
This review provides information on available methods for engineering glycan-binding proteins (GBP). Glycans are involved in a variety of physiological functions and are found in all domains of life and viruses. Due to their wide range of functions, GBPs have been developed with diagnostic, therapeutic, and biotechnological applications. The development of GBPs has traditionally been hindered by a lack of available glycan targets and sensitive and selective protein scaffolds; however, recent advances in glycobiology have largely overcome these challenges. Here we provide information on how to approach the design of novel "designer" GBPs, starting from the protein scaffold to the mutagenesis methods, selection, and characterization of the GBPs.
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Affiliation(s)
- Ruben Warkentin
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - David H. Kwan
- Department of Biology, Centre for Applied Synthetic Biology, and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada;
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada
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3
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Abstract
Formation of carbon-carbon bonds is central to synthetic chemistry. The aldol reaction provides the chemistry to fuse a nucleophilic enolate with an electrophilic aldehyde to form a new CC bond between two newly formed asymmetric centers. A major challenge in the reaction is steering the stereochemistry of the product. Aldolases are lyases that catalyze aldol reactions as well as the retro-aldol cleavage, and are abundant in cellular metabolism. Due to the often exquisite stereoselectivity in aldolase catalyzed carboligation reactions, these enzymes are gaining increased interest as potentially important tools in asymmetric synthesis of new useful compounds. Fructose 6-phosphate aldolase from Escherichia coli (FSA) is of special interest because of its very unusual independence of phosphorylated reactant substrates. The current text describes the protein engineering of FSA, applying principles of directed evolution, for the generation, production and characterization of new aldolase variants. A range of new enantiopure polyhydroxylated compounds were produced applying isolated FSA variants.
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Affiliation(s)
- Mikael Widersten
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
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4
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Hernández K, Gómez A, Joglar J, Bujons J, Parella T, Clapés P. 2-Keto-3-Deoxy-l-Rhamnonate Aldolase (YfaU) as Catalyst in Aldol Additions of Pyruvate to Amino Aldehyde Derivatives. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700360] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Karel Hernández
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ariadna Gómez
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jesús Joglar
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear; Facultat de Ciències; Universitat Autònoma de Barcelona; 08193 Cerdanyola del Vallès Barcelona Spain
| | - Pere Clapés
- Catalonia Institute for Advanced Chemistry - IQAC-CSIC; Department of Chemical Biology and Molecular Modelling; Jordi Girona 18-26 08034 Barcelona Spain
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Schmidt NG, Eger E, Kroutil W. Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products. ACS Catal 2016; 6:4286-4311. [PMID: 27398261 PMCID: PMC4936090 DOI: 10.1021/acscatal.6b00758] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/13/2016] [Indexed: 12/12/2022]
Abstract
Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.
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Affiliation(s)
- Nina G. Schmidt
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
| | - Elisabeth Eger
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
| | - Wolfgang Kroutil
- ACIB
GmbH c/o, Department of Chemistry, University
of Graz, Heinrichstrasse
28, 8010 Graz, Austria
- Department
of Chemistry, Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, 8010 Graz, Austria
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6
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Xia PF, Zhang GC, Liu JJ, Kwak S, Tsai CS, Kong II, Sung BH, Sohn JH, Wang SG, Jin YS. GroE chaperonins assisted functional expression of bacterial enzymes inSaccharomyces cerevisiae. Biotechnol Bioeng 2016; 113:2149-55. [DOI: 10.1002/bit.25980] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 01/31/2023]
Affiliation(s)
- Peng-Fei Xia
- School of Environmental Science and Engineering; Shandong University; Jinan P.R. China
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Guo-Chang Zhang
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; 905 South Goodwin Avenue Urbana Illinois 61801
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - Suryang Kwak
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; 905 South Goodwin Avenue Urbana Illinois 61801
| | - Ching-Sung Tsai
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
| | - In Iok Kong
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; 905 South Goodwin Avenue Urbana Illinois 61801
| | - Bong Hyun Sung
- Bioenergy and Biochemical Research Center; Korea Research Institute of Bioscience and Biotechnology; Daejeon Korea
| | - Jung-Hoon Sohn
- Bioenergy and Biochemical Research Center; Korea Research Institute of Bioscience and Biotechnology; Daejeon Korea
| | - Shu-Guang Wang
- School of Environmental Science and Engineering; Shandong University; Jinan P.R. China
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology; University of Illinois at Urbana-Champaign; Urbana Illinois
- Department of Food Science and Human Nutrition; University of Illinois at Urbana-Champaign; 905 South Goodwin Avenue Urbana Illinois 61801
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Kang YS, Song JA, Han KY, Lee J. Escherichia coli EDA is a novel fusion expression partner to improve solubility of aggregation-prone heterologous proteins. J Biotechnol 2015; 194:39-47. [DOI: 10.1016/j.jbiotec.2014.11.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 01/26/2023]
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8
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Steady-state hydrogen peroxide induces glycolysis in Staphylococcus aureus and Pseudomonas aeruginosa. J Bacteriol 2014; 196:2499-513. [PMID: 24769698 DOI: 10.1128/jb.01538-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from human pathogens Staphylococcus aureus and Pseudomonas aeruginosa can be readily inhibited by reactive oxygen species (ROS)-mediated direct oxidation of their catalytic active cysteines. Because of the rapid degradation of H2O2 by bacterial catalase, only steady-state but not one-dose treatment with H2O2 rapidly induces glycolysis and the pentose phosphate pathway (PPP). We conducted transcriptome sequencing (RNA-seq) analyses to globally profile the bacterial transcriptomes in response to a steady level of H2O2, which revealed profound transcriptional changes, including the induced expression of glycolytic genes in both bacteria. Our results revealed that the inactivation of GAPDH by H2O2 induces metabolic levels of glycolysis and the PPP; the elevated levels of fructose 1,6-biphosphate (FBP) and 2-keto-3-deoxy-6-phosphogluconate (KDPG) lead to dissociation of their corresponding glycolytic repressors (GapR and HexR, respectively) from their cognate promoters, thus resulting in derepression of the glycolytic genes to overcome H2O2-stalled glycolysis in S. aureus and P. aeruginosa, respectively. Both GapR and HexR may directly sense oxidative stresses, such as menadione.
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9
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Benisch F, Boles E. The bacterial Entner–Doudoroff pathway does not replace glycolysis in Saccharomyces cerevisiae due to the lack of activity of iron–sulfur cluster enzyme 6-phosphogluconate dehydratase. J Biotechnol 2014; 171:45-55. [DOI: 10.1016/j.jbiotec.2013.11.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/02/2013] [Accepted: 11/22/2013] [Indexed: 01/04/2023]
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Windle CL, Müller M, Nelson A, Berry A. Engineering aldolases as biocatalysts. Curr Opin Chem Biol 2014; 19:25-33. [PMID: 24780276 PMCID: PMC4012138 DOI: 10.1016/j.cbpa.2013.12.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 11/30/2022]
Abstract
Aldolases are seen as an attractive route to the production of biologically important compounds due to their ability to form carbon-carbon bonds. However, for many industrial reactions there are no naturally occurring enzymes, and so many different engineering approaches have been used to address this problem. Engineering methods have been used to alter the stability, substrate specificity and stereospecificity of aldolases to produce excellent enzymes for biocatalytic processes. Recently greater understanding of the aldolase mechanism has allowed many successes with both rational engineering approaches and computational design of aldolases. Rational engineering approaches have produced desired enzymes quickly and efficiently while combination of computational design with laboratory methods has created enzymes with activity approaching that of natural enzymes.
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Affiliation(s)
- Claire L Windle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Marion Müller
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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12
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Widmann M, Pleiss J, Samland AK. Computational tools for rational protein engineering of aldolases. Comput Struct Biotechnol J 2012; 2:e201209016. [PMID: 24688657 PMCID: PMC3962226 DOI: 10.5936/csbj.201209016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/31/2012] [Accepted: 11/07/2012] [Indexed: 11/22/2022] Open
Abstract
In this mini-review we describe the different strategies for rational protein engineering and summarize the computational tools available. Computational tools can either be used to design focused libraries, to predict sequence-function relationships or for structure-based molecular modelling. This also includes de novo design of enzymes. Examples for protein engineering of aldolases and transaldolases are given in the second part of the mini-review.
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Affiliation(s)
- Michael Widmann
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Anne K Samland
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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Cheriyan M, Toone EJ, Fierke CA. Improving upon nature: active site remodeling produces highly efficient aldolase activity toward hydrophobic electrophilic substrates. Biochemistry 2012; 51:1658-68. [PMID: 22316217 DOI: 10.1021/bi201899b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The substrate specificity of enzymes is frequently narrow and constrained by multiple interactions, limiting the use of natural enzymes in biocatalytic applications. Aldolases have important synthetic applications, but the usefulness of these enzymes is hampered by their narrow reactivity profile with unnatural substrates. To explore the determinants of substrate selectivity and alter the specificity of Escherichia coli 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, we employed structure-based mutagenesis coupled with library screening of mutant enzymes localized to the bacterial periplasm. We identified two active site mutations (T161S and S184L) that work additively to enhance the substrate specificity of this aldolase to include catalysis of retro-aldol cleavage of (4S)-2-keto-4-hydroxy-4-(2'-pyridyl)butyrate (S-KHPB). These mutations improve the value of k(cat)/K(M)(S-KHPB) by >450-fold, resulting in a catalytic efficiency that is comparable to that of the wild-type enzyme with the natural substrate while retaining high stereoselectivity. Moreover, the value of k(cat)(S-KHPB) for this mutant enzyme, a parameter critical for biocatalytic applications, is 3-fold higher than the maximal value achieved by the natural aldolase with any substrate. This mutant also possesses high catalytic efficiency for the retro-aldol cleavage of the natural substrate, KDPG, and a >50-fold improved activity for cleavage of 2-keto-4-hydroxy-octonoate, a nonfunctionalized hydrophobic analogue. These data suggest a substrate binding mode that illuminates the origin of facial selectivity in aldol addition reactions catalyzed by KDPG and 2-keto-3-deoxy-6-phosphogalactonate aldolases. Furthermore, targeting mutations to the active site provides a marked improvement in substrate selectivity, demonstrating that structure-guided active site mutagenesis combined with selection techniques can efficiently identify proteins with characteristics that compare favorably to those of naturally occurring enzymes.
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Affiliation(s)
- Manoj Cheriyan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Structural and biochemical studies of human 4-hydroxy-2-oxoglutarate aldolase: implications for hydroxyproline metabolism in primary hyperoxaluria. PLoS One 2011; 6:e26021. [PMID: 21998747 PMCID: PMC3188589 DOI: 10.1371/journal.pone.0026021] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/15/2011] [Indexed: 11/19/2022] Open
Abstract
Background 4-hydroxy-2-oxoglutarate (HOG) aldolase is a unique enzyme in the hydroxyproline degradation pathway catalyzing the cleavage of HOG to pyruvate and glyoxylate. Mutations in this enzyme are believed to be associated with the excessive production of oxalate in primary hyperoxaluria type 3 (PH3), although no experimental data is available to support this hypothesis. Moreover, the identity, oligomeric state, enzymatic activity, and crystal structure of human HOGA have not been experimentally determined. Methodology/Principal Findings In this study human HOGA (hHOGA) was identified by mass spectrometry of the mitochondrial enzyme purified from bovine kidney. hHOGA performs a retro-aldol cleavage reaction reminiscent of the trimeric 2-keto-3-deoxy-6-phosphogluconate aldolases. Sequence comparisons, however, show that HOGA is related to the tetrameric, bacterial dihydrodipicolinate synthases, but the reaction direction is reversed. The 1.97 Å resolution crystal structure of hHOGA bound to pyruvate was determined and enabled the modeling of the HOG-Schiff base intermediate and the identification of active site residues. Kinetic analyses of site-directed mutants support the importance of Lys196 as the nucleophile, Tyr168 and Ser77 as components of a proton relay, and Asn78 and Ser198 as unique residues that facilitate substrate binding. Conclusions/Significance The biochemical and structural data presented support that hHOGA utilizes a type I aldolase reaction mechanism, but employs novel residue interactions for substrate binding. A mapping of the PH3 mutations identifies potential rearrangements in either the active site or the tetrameric assembly that would likely cause a loss in activity. Altogether, these data establish a foundation to assess mutant forms of hHOGA and how their activity could be pharmacologically restored.
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15
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Cheriyan M, Walters MJ, Kang BD, Anzaldi LL, Toone EJ, Fierke CA. Directed evolution of a pyruvate aldolase to recognize a long chain acyl substrate. Bioorg Med Chem 2011; 19:6447-53. [PMID: 21944547 DOI: 10.1016/j.bmc.2011.08.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 08/19/2011] [Accepted: 08/26/2011] [Indexed: 11/29/2022]
Abstract
The use of biological catalysts for industrial scale synthetic chemistry is highly attractive, given their cost effectiveness, high specificity that obviates the need for protecting group chemistry, and the environmentally benign nature of enzymatic procedures. Here we evolve the naturally occurring 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolases from Thermatoga maritima and Escherichia coli, into enzymes that recognize a nonfunctionalized electrophilic substrate, 2-keto-4-hydroxyoctonoate (KHO). Using an in vivo selection based on pyruvate auxotrophy, mutations were identified that lower the K(M) value up to 100-fold in E. coli KDPG aldolase, and that enhance the efficiency of retro-aldol cleavage of KHO by increasing the value of k(cat)/K(M) up to 25-fold in T. maritima KDPG aldolase. These data indicate that numerous mutations distal from the active site contribute to enhanced 'uniform binding' of the substrates, which is the first step in the evolution of novel catalytic activity.
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Affiliation(s)
- Manoj Cheriyan
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Tang KH, Tang YJ, Blankenship RE. Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. Front Microbiol 2011; 2:165. [PMID: 21866228 PMCID: PMC3149686 DOI: 10.3389/fmicb.2011.00165] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/18/2011] [Indexed: 11/19/2022] Open
Abstract
Photosynthesis is the biological process that converts solar energy to biomass, bio-products, and biofuel. It is the only major natural solar energy storage mechanism on Earth. To satisfy the increased demand for sustainable energy sources and identify the mechanism of photosynthetic carbon assimilation, which is one of the bottlenecks in photosynthesis, it is essential to understand the process of solar energy storage and associated carbon metabolism in photosynthetic organisms. Researchers have employed physiological studies, microbiological chemistry, enzyme assays, genome sequencing, transcriptomics, and (13)C-based metabolomics/fluxomics to investigate central carbon metabolism and enzymes that operate in phototrophs. In this report, we review diverse CO(2) assimilation pathways, acetate assimilation, carbohydrate catabolism, the tricarboxylic acid cycle and some key, and/or unconventional enzymes in central carbon metabolism of phototrophic microorganisms. We also discuss the reducing equivalent flow during photoautotrophic and photoheterotrophic growth, evolutionary links in the central carbon metabolic network, and correlations between photosynthetic and non-photosynthetic organisms. Considering the metabolic versatility in these fascinating and diverse photosynthetic bacteria, many essential questions in their central carbon metabolism still remain to be addressed.
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Affiliation(s)
- Kuo-Hsiang Tang
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
| | - Yinjie J. Tang
- Department of Energy, Environment, and Chemical Engineering, Washington University in St. LouisSt. Louis, MO, USA
| | - Robert Eugene Blankenship
- Department of Biology, Washington University in St. LouisSt. Louis, MO, USA
- Department of Chemistry, Washington University in St. LouisSt. Louis, MO, USA
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18
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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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19
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Garrabou X, Joglar J, Parella T, Crehuet R, Bujons J, Clapés P. Redesign of the Phosphate Binding Site of L-Rhamnulose- 1-Phosphate Aldolase towards a Dihydroxyacetone Dependent Aldolase. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201000719] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Royer SF, Haslett L, Crennell SJ, Hough DW, Danson MJ, Bull SD. Structurally Informed Site-Directed Mutagenesis of a Stereochemically Promiscuous Aldolase To Afford Stereochemically Complementary Biocatalysts. J Am Chem Soc 2010; 132:11753-8. [DOI: 10.1021/ja104412a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sylvain F. Royer
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Luke Haslett
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Susan J. Crennell
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - David W. Hough
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Michael J. Danson
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
| | - Steven D. Bull
- Centre for Extremophile Research, Department of Biology and Biochemistry, and Department of Chemistry, University of Bath, Bath, United Kingdom BA2 7AY
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Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Characterization and crystal structure of Escherichia coli KDPGal aldolase. Bioorg Med Chem 2008; 16:710-20. [PMID: 17981470 PMCID: PMC3326530 DOI: 10.1016/j.bmc.2007.10.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 10/05/2007] [Accepted: 10/12/2007] [Indexed: 11/29/2022]
Abstract
2-Keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases catalyze an identical reaction differing in substrate specificity in only the configuration of a single stereocenter. However, the proteins show little sequence homology at the amino acid level. Here we investigate the determinants of substrate selectivity of these enzymes. The Escherichia coli KDPGal aldolase gene, cloned into a T7 expression vector and overexpressed in E. coli, catalyzes retro-aldol cleavage of the natural substrate, KDPGal, with values of k(cat)/K(M) and k(cat) of 1.9x10(4)M(-1)s(-1) and 4s(-1), respectively. In the synthetic direction, KDPGal aldolase efficiently catalyzes an aldol addition using a limited number of aldehyde substrates, including d-glyceraldehyde-3-phosphate (natural substrate), d-glyceraldehyde, glycolaldehyde, and 2-pyridinecarboxaldehyde. A preparative scale reaction between 2-pyridinecarboxaldehyde and pyruvate catalyzed by KDPGal aldolase produced the aldol adduct of the R stereochemistry in >99.7% ee, a result complementary to that observed using the related KDPG aldolase. The native crystal structure has been solved to a resolution of 2.4A and displays the same (alpha/beta)(8) topology, as KDPG aldolase. We have also determined a 2.1A structure of a Schiff base complex between the enzyme and its substrate. This model predicts that a single amino acid change, T161 in KDPG aldolase to V154 in KDPGal aldolase, plays an important role in determining the stereochemical course of enzyme catalysis and this prediction was borne out by site-directed mutagenesis studies. However, additional changes in the enzyme sequence are required to prepare an enzyme with both high catalytic efficiency and altered stereochemistry.
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Affiliation(s)
- Matthew J Walters
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Walters MJ, Srikannathasan V, McEwan AR, Naismith JH, Fierke CA, Toone EJ. Mechanism of the Class I KDPG aldolase. Bioorg Med Chem 2006; 14:3002-10. [PMID: 16403639 PMCID: PMC3315828 DOI: 10.1016/j.bmc.2005.12.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 12/04/2005] [Accepted: 12/09/2005] [Indexed: 11/17/2022]
Abstract
In vivo, 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible, stereospecific retro-aldol cleavage of KDPG to pyruvate and D-glyceraldehyde-3-phosphate. The enzyme is a lysine-dependent (Class I) aldolase that functions through the intermediacy of a Schiff base. Here, we propose a mechanism for this enzyme based on crystallographic studies of wild-type and mutant aldolases. The three dimensional structure of KDPG aldolase from the thermophile Thermotoga maritima was determined to 1.9A. The structure is the standard alpha/beta barrel observed for all Class I aldolases. At the active site Lys we observe clear density for a pyruvate Schiff base. Density for a sulfate ion bound in a conserved cluster of residues close to the Schiff base is also observed. We have also determined the structure of a mutant of Escherichia coli KDPG aldolase in which the proposed general acid/base catalyst has been removed (E45N). One subunit of the trimer contains density suggesting a trapped pyruvate carbinolamine intermediate. All three subunits contain a phosphate ion bound in a location effectively identical to that of the sulfate ion bound in the T. maritima enzyme. The sulfate and phosphate ions experimentally locate the putative phosphate binding site of the aldolase and, together with the position of the bound pyruvate, facilitate construction of a model for the full-length KDPG substrate complex. The model requires only minimal positional adjustments of the experimentally determined covalent intermediate and bound anion to accommodate full-length substrate. The model identifies the key catalytic residues of the protein and suggests important roles for two observable water molecules. The first water molecule remains bound to the enzyme during the entire catalytic cycle, shuttling protons between the catalytic glutamate and the substrate. The second water molecule arises from dehydration of the carbinolamine and serves as the nucleophilic water during hydrolysis of the enzyme-product Schiff base. The second water molecule may also mediate the base-catalyzed enolization required to form the carbon nucleophile, again bridging to the catalytic glutamate. Many aspects of this mechanism are observed in other Class I aldolases and suggest a mechanistically and, perhaps, evolutionarily related family of aldolases distinct from the N-acetylneuraminate lyase (NAL) family.
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Affiliation(s)
- Matthew J. Walters
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Andrew R. McEwan
- Centre for Biomolecular Sciences, The University of St. Andrews, St. Andrews KY169ST, UK
| | - James H. Naismith
- Centre for Biomolecular Sciences, The University of St. Andrews, St. Andrews KY169ST, UK
| | - Carol A. Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48103, USA
| | - Eric J. Toone
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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