Insight into a natural Diels–Alder reaction from the structure of macrophomate synthase

Ose, Toyoyuki; Watanabe, Kenji; Mie, Takashi; Honma, Mamoru; Watanabe, Hiromi; Yao, Min; Oikawa, Hideaki; Tanaka, Isao

doi:10.1038/nature01454

Cited by 191 publications

(180 citation statements)

References 27 publications

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“…As such, surface ligands on noble metal nanocatalysts may provide a similar orientation effect to improve the product selectivity through molecule recognition and/or specific regulation on adsorption. One straightforward way is to utilize the structural and chemical similarity of reactants and ligands that potentially can orient reactants through an enthalpy-driven path [45][46][47].…”

Section: Orientation Effect Of Surface Ligandsmentioning

confidence: 99%

Engineering Surface Ligands of Noble Metal Nanocatalysts in Tuning the Product Selectivity

Liu

Duay

et al. 2017

Catalysts

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Nanosized noble metal catalysts supported on high-surface-area support are of great importance for numerous industrial chemical processes to mediate reaction pathways in heterogeneous catalysis. Control of surface area and surface energy of nanocatalysts is a key to achieving high activity and selectivity for desired products. In the past decade, new synthetic methodologies for noble metal nanocatalysts with well-defined nanostructures have been developed. Wet-chemical preparation of noble metal nanocatalysts usually involves the utilization of specific surfactants that can bind the surface of nanocatalysts as ligands to control the nanostructures and prevent the coalescence of nanocatalysts. Surface ligands that form a densely packed self-assembled monolayer offer a facile solution to tune the surface energy of nanocatalysts, and, therefore, the selectivity of products. In this minireview, we highlight the recent advances in understanding the role of surface ligands in control over the product selectivity in a multi-product reaction using noble metal nanocatalysts. The review is outlined according to the three possible roles of surface ligands, including steric effect, orientation effect and surface charge state, in varying the adsorption/binding of reactants/transition states.

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Section: Orientation Effect Of Surface Ligandsmentioning

confidence: 99%

Engineering Surface Ligands of Noble Metal Nanocatalysts in Tuning the Product Selectivity

Liu

Duay

et al. 2017

Catalysts

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“…Major differences, however, lie in the use of a bound Mg 2+ cation, which directly coordinates to the carbonyl oxygens of the dienophile and participates in the catalytic mechanism, and in the generally lower importance of stacking in enzyme-substrate interactions 42,43 .…”

Section: Comparison With Protein-catalyzed Reactionsmentioning

confidence: 99%

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

Serganov

Keiper

Malinina

et al. 2005

Nat Struct Mol Biol

191

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The majority of structural efforts addressing RNA's catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme-and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions.The discovery of the catalytic activity of RNA 1,2 and the hypothesis of a prebiotic 'RNA world' 3 have expanded the scope of enzymology to include other biopolymers than proteins. The currently known natural ribozymes catalyze only a narrow range of chemical reactions, namely the hydrolysis and transesterification of internucleotide bonds 4,5 , and probably peptide bond formation 6 . However, in vitro selection and evolution have demonstrated that ribozymes are capable of accelerating a much broader reaction spectrum 7 . This finding and Correspondence should be addressed to A.J. (jaeschke@uni-hd.de) or D.J.P. (pateld@mskcc.org). COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests.Note: Supplementary information is available on the Nature Structural & Molecular Biology website. HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript recent discoveries of metabolite-controlled RNA switches and ribozymes 8,9 suggest that RNA might have performed an even broader range of activities in the preprotein realm, and that in vitro-selected ribozymes could be analogs of the missing links in the transition from an RNA world to modern protein-dominated life 10 . Whereas high-resolution structures and biochemical investigations of several natural ribozymes provide a basic understanding of how RNA carries out phosphodiester chemistry 5,11 , little is known about how RNA catalyzes other reactions. To obtain a comprehensive picture of the catalytic abilities and limitations of ribozymes, it is thus important to expand structural and mechanistic investigations to in vitro-selected ribozymes [12][13][14] . Such structural information can be especially valuable in the determination of the minimal RNA folds required for catalysis and, therefore, could be helpful in the investigation of the origin and evolution of natural ribozymes 15 .Two examples describe the in vitro selection of ribozymes that accelerate the formation of ...

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“…[13] This reaction type is of great relevance in organic chemistry, [14] and candidates for catalyzing the Diels-Alder reaction in nature are currently under intensive investigation. [15][16][17] This ribozyme was the first RNA enzyme to catalyze a bond-forming reaction enantioselectively, [18] and substrate-specificity studies suggested a simple and convincing structural model for the stereoselectivity (Figure 1b). [19] The size of the diene's substituent was identified as the major determinant of stereoselectivity (see the table in Figure 1), and the diene was thought to enter the catalytic pocket with the sterically less demanding edge first, then react with the maleimide bound in one fixed orientation (Figure 1b, left model), while the opposite orientation of the anthracene (right model) was found to be disfavored.…”

mentioning

confidence: 98%

Control of Stereoselectivity in an Enzymatic Reaction by Backdoor Access

et al. 2006

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The ability of biopolymers to discriminate between optical isomers is vital for living systems, and the selective formation of only one product stereoisomer from achiral substrates is one of the most sophisticated tasks for enzymes. Using a Diels-Alder ribozyme as an example, we demonstrate here that by a simple strategy a biocatalyst can be used to selectively synthesize both product stereoisomers in one catalytic pocket, namely, by controlling access to the active site from opposite directions through different "doors". While substrates tethered to the catalyst were used to observe this phenomenon, we propose ** We gratefully acknowledge support by the Bundesministerium für Bildung und Forschung (BioFuture program), the Deutsche Forschungsgemeinschaft, and the Human Frontiers Science Program (A.J.), and by the NIH, the DeWitt Wallace Foundation, and the Abby Rockefeller Mauze Trust (D.J.P.).

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Insight into a natural Diels–Alder reaction from the structure of macrophomate synthase

Cited by 191 publications

References 27 publications

Engineering Surface Ligands of Noble Metal Nanocatalysts in Tuning the Product Selectivity

Engineering Surface Ligands of Noble Metal Nanocatalysts in Tuning the Product Selectivity

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

Control of Stereoselectivity in an Enzymatic Reaction by Backdoor Access

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