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Remmerswaal WA, Hansen T, Hamlin TA, Codée JDC. Origin of Stereoselectivity in S E 2' Reactions of Six-membered Ring Oxocarbenium Ions. Chemistry 2023; 29:e202203490. [PMID: 36511875 DOI: 10.1002/chem.202203490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Oxocarbenium ions are key reactive intermediates in organic chemistry. To generate a series of structure-reactivity-stereoselectivity principles for these species, we herein investigated the bimolecular electrophilic substitution reactions (SE 2') between allyltrimethylsilane and a series of archetypal six-membered ring oxocarbenium ions using a combined density functional theory (DFT) and coupled-cluster theory approach. These reactions preferentially proceed following a reaction path where the oxocarbenium ion transforms from a half chair (3 H4 or 4 H3 ) to a chair conformation. The introduction of alkoxy substituents on six-membered ring oxocarbenium ions, dramatically influences the conformational preference of the canonical 3 H4 and 4 H3 conformers, and thereby the stereochemical outcome of the SE 2' reaction. In general, we find that the stereoselectivity in the reactions correlates to the "intrinsic preference" of the cations, as dictated by their shape. However, for the C5-CH2 OMe substituent, steric factors override the "intrinsic preference", showing a more selective reaction than expected based on the shape of the ion. Our SE 2' energetics correlate well with experimentally observed stereoselectivity, and the use of the activation strain model has enabled us to quantify important interactions and structural features that occur in the transition state of the reactions to precisely understand the relative energy barriers of the diastereotopic addition reactions. The fundamental mechanistic insight provided in this study will aid in understanding the reactivity of more complex glycosyl cations featuring multiple substituents and will facilitate our general understanding of glycosylation reactions.
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Affiliation(s)
- Wouter A Remmerswaal
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
| | - Thomas Hansen
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands.,Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam (The, Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The, Netherlands
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2
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Yan L, Liu Y. The Retaining Mechanism of Xylose Transfer Catalyzed by Xyloside α-1,3-Xylosyltransferase (XXYLT1): a Quantum Mechanics/Molecular Mechanics Study. J Chem Inf Model 2020; 60:1585-1594. [PMID: 32105482 DOI: 10.1021/acs.jcim.9b00976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosyltransferases (GTs) are a ubiquitous group of enzymes that catalyze the synthesis of glycosidic bonds. In this work, we focused on the retained reaction catalyzed by xyloside α-1,3-xylosyltransferase (XXYLT1) from Mus musculus. Our calculations revealed that the xylose transfer reaction follows the SNi-like mechanism, which involves a short-lived oxocarbenium-phosphate ion-pair intermediate (IP). The previously obtained crystal structure of the UDP-Xyl ternary Michaelis reaction complex was found to be an inactive form. Accordingly, the β-phosphate oxygen O3B of the donor should first undergo a conformational change to reach an active state where the donor forms a strong hydrogen bond with the acceptor, facilitating the departure of the phosphate group. Our calculations also revealed that two predicated transition states for the sugar-phosphate bond cleavage and glycosidic bond formation are structurally similar to the short-lived intermediate, which contains a three-member ring formed by the β-phosphate oxygen, the hydroxyl oxygen in the acceptor, and the anomeric carbon. It can be considered as a typical characteristic of the SNi-like mechanism. In addition, a nearby polar residue, Q330, is responsible for stabilizing the short-lived intermediate by electrostatic interactions. Thus, the Q330A mutant can abolish the activity of XXYLT1. In addition, using UDP-glucose as the donor, our calculations revealed that glucose transfer would correspond to a higher energy barrier owing to the steric repulsion between the glucosyl moiety and the nearby residue L327, indicating the requirement of active site architecture for glucose transfer. These findings not only explain the experimental observations but also are meaningful for clarifying the mechanism of GTs.
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Affiliation(s)
- Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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Albesa‐Jové D, Mendoza F, Rodrigo‐Unzueta A, Gomollón‐Bel F, Cifuente JO, Urresti S, Comino N, Gómez H, Romero‐García J, Lluch JM, Sancho‐Vaello E, Biarnés X, Planas A, Merino P, Masgrau L, Guerin ME. A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase. Angew Chem Int Ed Engl 2015; 54:9898-902. [DOI: 10.1002/anie.201504617] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Indexed: 12/29/2022]
Affiliation(s)
- David Albesa‐Jové
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas ‐ Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC‐UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain)
- IKERBASQUE, 48013 Bilbao (Spain)
| | - Fernanda Mendoza
- IBB and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Spain)
| | - Ane Rodrigo‐Unzueta
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas ‐ Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC‐UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain)
| | - Fernando Gomollón‐Bel
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009 Zaragoza, Aragón (Spain)
| | - Javier O. Cifuente
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas ‐ Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC‐UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain)
| | - Saioa Urresti
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas ‐ Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC‐UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain)
| | - Natalia Comino
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas ‐ Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC‐UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain)
| | - Hansel Gómez
- IBB and Joint BSC‐CRG‐IRB Program in Computational Biology, IRB Barcelona, 08028 Barcelona (Spain)
| | - Javier Romero‐García
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona (Spain)
| | - José M. Lluch
- IBB and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Spain)
| | - Enea Sancho‐Vaello
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas ‐ Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC‐UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain)
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona (Spain)
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona (Spain)
| | - Pedro Merino
- Laboratorio de Síntesis Asimétrica, Departamento de Síntesis y Estructura de Biomoléculas, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza, CSIC, 50009 Zaragoza, Aragón (Spain)
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina (IBB) (Spain)
| | - Marcelo E. Guerin
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas ‐ Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC‐UPV/EHU) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Bizkaia (Spain)
- IKERBASQUE, 48013 Bilbao (Spain)
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Albesa-Jové D, Mendoza F, Rodrigo-Unzueta A, Gomollón-Bel F, Cifuente JO, Urresti S, Comino N, Gómez H, Romero-García J, Lluch JM, Sancho-Vaello E, Biarnés X, Planas A, Merino P, Masgrau L, Guerin ME. A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Lira-Navarrete E, Iglesias-Fernández J, Zandberg WF, Compañón I, Kong Y, Corzana F, Pinto BM, Clausen H, Peregrina JM, Vocadlo DJ, Rovira C, Hurtado-Guerrero R. Substrate-guided front-face reaction revealed by combined structural snapshots and metadynamics for the polypeptide N-acetylgalactosaminyltransferase 2. Angew Chem Int Ed Engl 2014; 53:8206-10. [PMID: 24954443 DOI: 10.1002/anie.201402781] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/19/2014] [Indexed: 12/16/2023]
Abstract
The retaining glycosyltransferase GalNAc-T2 is a member of a large family of human polypeptide GalNAc-transferases that is responsible for the post-translational modification of many cell-surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum-mechanics/molecular-mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic-electronic level of detail. Our study provides a detailed structural rationale for an ordered bi-bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front-face SN i-type reaction in which the substrate N-acetyl sugar substituent coordinates efficient glycosyl transfer.
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Affiliation(s)
- Erandi Lira-Navarrete
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Fundacion ARAID, Edificio Pignatelli 36 (Spain)
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Lira-Navarrete E, Iglesias-Fernández J, Zandberg WF, Compañón I, Kong Y, Corzana F, Pinto BM, Clausen H, Peregrina JM, Vocadlo DJ, Rovira C, Hurtado-Guerrero R. Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the PolypeptideN-Acetylgalactosaminyltransferase 2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402781] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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7
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Cantu DC, Ardèvol A, Rovira C, Reilly PJ. Molecular mechanism of a hotdog-fold acyl-CoA thioesterase. Chemistry 2014; 20:9045-51. [PMID: 24894958 DOI: 10.1002/chem.201304228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 04/22/2014] [Indexed: 11/10/2022]
Abstract
Thioesterases are enzymes that hydrolyze thioester bonds between a carbonyl group and a sulfur atom. They catalyze key steps in fatty acid biosynthesis and metabolism, as well as polyketide biosynthesis. The reaction molecular mechanism of most hotdog-fold acyl-CoA thioesterases remains unknown, but several hypotheses have been put forward in structural and biochemical investigations. The reaction of a human thioesterase (hTHEM2), representing a thioesterase family with a hotdog fold where a coenzyme A moiety is cleaved, was simulated by quantum mechanics/molecular mechanics metadynamics techniques to elucidate atomic and electronic details of its mechanism, its transition-state conformation, and the free energy landscape of the process. A single-displacement acid-base-like mechanism, in which a nucleophilic water molecule is activated by an aspartate residue acting as a base, was found, confirming previous experimental proposals. The results provide unambiguous evidence of the formation of a tetrahedral-like transition state. They also explain the roles of other conserved active-site residues during the reaction, especially that of a nearby histidine/serine pair that protonates the thioester sulfur atom, the participation of which could not be elucidated from mutation analyses alone.
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Affiliation(s)
- David C Cantu
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230 (USA)
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Rojas-Cervellera V, Ardèvol A, Boero M, Planas A, Rovira C. Formation of a covalent glycosyl-enzyme species in a retaining glycosyltransferase. Chemistry 2013; 19:14018-23. [PMID: 24108590 DOI: 10.1002/chem.201302898] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Indexed: 01/11/2023]
Abstract
Elusive glycosyl-enzyme adduct: Using classical MD simulations and QM/MM metadynamics, the long-time sought glycosyl-enzyme covalent intermediate of a retaining glycosyltransferase, with a putative nucleophile residue in the active site, has been trapped (MD=molecular dynamics; QM/MM=quantum mechanics/molecular mechanics).
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Affiliation(s)
- Víctor Rojas-Cervellera
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Diagonal 647, 08028 Barcelona (Spain)
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9
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Thompson AJ, Dabin J, Iglesias-Fernández J, Ardèvol A, Dinev Z, Williams SJ, Bande O, Siriwardena A, Moreland C, Hu TC, Smith DK, Gilbert HJ, Rovira C, Davies GJ. The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach. Angew Chem Int Ed Engl 2012; 51:10997-1001. [DOI: 10.1002/anie.201205338] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Indexed: 11/10/2022]
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10
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Thompson AJ, Dabin J, Iglesias-Fernández J, Ardèvol A, Dinev Z, Williams SJ, Bande O, Siriwardena A, Moreland C, Hu TC, Smith DK, Gilbert HJ, Rovira C, Davies GJ. The Reaction Coordinate of a Bacterial GH47 α-Mannosidase: A Combined Quantum Mechanical and Structural Approach. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205338] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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