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Substrate‐Guided Front‐Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N‐Acetylgalactosaminyltransferase 2 |
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| Authors: | Dr. Wesley F. Zandberg Ismael Compañón Yun Kong Dr. Francisco Corzana Prof. B. Mario Pinto Prof. Henrik Clausen Prof. Jesús M. Peregrina Prof. David J. Vocadlo Prof. Carme Rovira Dr. Ramon Hurtado‐Guerrero |
| Affiliation: | 1. Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC (Canada);2. Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, Logro?o (Spain);3. Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen (Denmark);4. Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, Barcelona (Spain);5. Institució Catalana de Recerca i Estudis Avan?ats (ICREA), Passeig Lluís Companys 23, 08020 Barcelona (Spain);6. 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) |
| 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 SNi‐type reaction in which the substrate N‐acetyl sugar substituent coordinates efficient glycosyl transfer. |
| Keywords: | acetamido groups proteins quantum mechanics/molecular mechanics SNi‐type reactions X‐ray diffraction |