DOI: 10.5281/zenodo.7704778
title: Supplementary Data for "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase"

description: This dataset contains atomic coordinates of the molecular dynamics simulations described in "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase" by M. Alfonso-Prieto, I. Cuxart, G. Potocki-Véronèse, I. André and C. Rovira, published in ACS Catalysis (https://doi.org/10.1021/acscatal.3c00451). Further details on the setup of the simulations can be found in the Supplementary Information of the article. If you use this dataset, please cite this zenodo upload (https://doi.org/10.5281/zenodo.7704778), as well as the the original journal article (https://doi.org/10.1021/acscatal.3c00451). This dataset is organized in the following folders: <strong>Snapshots_Figures_Main_Text.zip</strong>, that contains a README.txt file and: <strong>- Figure_3</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP in complex with 3 different disaccharide molecules, Man-b-(1,4)-GlcNAc, Man-b-(1,4)-Glc and Man-b-(1,4)-Man. <strong>- Figure_4</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP at the three minima observed along the reaction coordinate corresponding to phosphorolysis of the disaccharide Man-b-(1,4)-GlcNAc: Michaelis complex (MC), transition state (TS) and product (P) complex. Files in this dataset are in PDB format. For all structures, the solvation box (water and ions) has been stripped to reduce file size. See README.txt inside Snapshots_Figures_Main_Text.zip for more information.
description: Funding: C.R. thanks the Spanish Ministry of Science, Innovation and Universities (MICINN/AEI/FEDER, UE, PID2020-118893GB-100), the Spanish Structures of Excellence María de Maeztu (MDM-2017-0767), the Agency for Management of University and Research Grants of Generalitat de Catalunya (AGAUR, 2017SGR-1189), and the Marie Skłodowska-Curie Innovative Training Networks (H2020-MSCA-ITN-2018–814102 "Sweet crosstalk" to C.R.). I.A. and G.P.-V. thank the French National Research Agency (ANR project OLIGOMET, ANR-16-CE20-0006-03) and the European Union's Horizon 2020 framework program (Grant FNR-2020-SEP-210639118, RadicalZ). The authors are thankful for the technical support provided by the Barcelona Supercomputing Center (BSC) and Red Nacional de Supercomputación (RES) for computer resources at MareNostrum IV and CTE-Power supercomputers (application project QH- 390 2022-3-0002). We are also grateful for the computer time provided on the TGCC-Curie supercomputer under the allocations t201608765 and A0030807565 and the Computing Mesocenter of Région Midi-Pyrénées (CALMIP, Toulouse, France) under allocation 16004. I.C. acknowledges a predoctoral fellowship from MICINN (ref. PRE2019- 396 089272). M.A.-P. acknowledges financial support from the Government of Catalonia (Commissioner for Universities and Research; Department of Innovation, Universities and Enterprise) and the European Union through a Beatriu de Pinós fellowship (BP-B 2013).
description: {"references": ["M. Alfonso-Prieto, I. Cuxart, G. Potocki-V\u00e9ron\u00e8se, I. Andr\u00e9, C. Rovira. Substrate-Assisted Mechanism for the Degradation of N\u2010Glycans by a Gut Bacterial Mannoside Phosphorylase. ACS Catalysis (2023) https://doi.org/10.1021/acscatal.3c00451"]}