Published March 10, 2023 | Version v1
Dataset Open

Supplementary Data for "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase"

Authors/Creators

  • 1. Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, 08028 Barcelona, Spain; Present Address: Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich 52425, Germany
  • 2. Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, 08028 Barcelona, Spain
  • 3. Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France. 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
  • 4. Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain

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:

Snapshots_Figures_Main_Text.zip, that contains a README.txt file and:

- Figure_3 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.

- Figure_4 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.

Notes

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).

Files

Snapshots_Figures_Main_Text.zip

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Additional details

Related works

Is supplement to
Journal article: 10.1021/acscatal.3c00451 (DOI)

References

  • M. Alfonso-Prieto, I. Cuxart, G. Potocki-Véronèse, I. André, C. Rovira. Substrate-Assisted Mechanism for the Degradation of N‐Glycans by a Gut Bacterial Mannoside Phosphorylase. ACS Catalysis (2023) https://doi.org/10.1021/acscatal.3c00451