Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide

DOI: 10.1002/ange.201402781

Authors: Erandi Lira (nstitute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza) , Javier Iglesias-fernández (Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona) , Wesley F. Zandberg (Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University) , Ismael Compañón (Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química) , Yun Kong (Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen) , Francisco Corzana (Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química) , B. Mario Pinto (Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University) , Henrik Clausen (Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, University of Copenhagen) , Jesús M. Peregrina (Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química) , David J. Vocadlo (Department of Chemistry and Department of Molecular Biology and Biochemistry, Simon Fraser University) , Carme Rovira (Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona) , Ramon Hurtado-guerrero (nstitute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Angewandte Chemie , VOL 126 , PAGES 8345 - 8349

State: Published (Approved)
Published: July 2014
Diamond Proposal Number(s): 8035

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.

Subject Areas: Chemistry


Instruments: I04-1-Macromolecular Crystallography (fixed wavelength) , I24-Microfocus Macromolecular Crystallography