Reaction mechanism of benzylsuccinate synthase - results of modeling and kinetic experiments

Published: 18 October 2024| Version 1 | DOI: 10.17632/ktkmtj3s4t.1
Contributors:
,
,
,
,
,

Description

The dataset collects results of the study on the reaction mechanism catalyzed by benzylsuccinate synthase (BSS) a fumarate-adding enzyme. Fumarate-adding enzymes (FAE) are a subset of the glycyl radical enzyme superfamily involved in anaerobic hydrocarbon degradation. Benzylsuccinate synthase catalyzes the enantiospecific formation of R-benzylsuccinate from toluene and fumarate, initiating anaerobic toluene degradation. In this deposition we collect crucial data from two papers: I) describing the initial step of the reaction i.e. hydrogen atom transfer from cysteine residue in the active site to glycyl radical which transfers radical close to the reagents and ii) description of the whole mechanism with QM:MM methods validated by prediction of kinetic isotope effect and enantioselectivity of the reaction. The first part of the data refers to the paper: M. Szaleniec et al., Modeling the Initiation Phase of the Catalytic Cycle in the Glycyl-Radical Enzyme Benzylsuccinate Synthase, The Journal of Physical Chemistry B 2024, 128, 24, 5823-5839 (https://doi.org/10.1021/acs.jpcb.4c01237). The data contains PDB structures of stationary states of the hydrogen atom transfer between Gly and Cys for the substrate and product bound enzyme as well as for the apoenzyme and AMBER parameters used to model BSS enzyme with radical Gly or Cys. The second part of the data refers to the preprint of the paper: M. Szaleniec et al., Unravelling the Enantioselective Mechanism of Benzylsuccinate Synthase: Insights into Anaerobic Hydrocarbon Degradation Through Multiscale Modelling and Kinetics, bioRxiv DOI: 10.1101/2024.10.11.617960. The data contains PDB structures of stationary states of the whole pathway (proR) and part of the proS pathway as well as results of kinetic experiments for both papers collected into an enzymeML spreadsheet. The enzymeML data contains results on KIE and HDX. Acknowledgements The authors acknowledge the financial support provided by Deutsche Forschungsgemeinschaft/National Science Center Poland under Beethoven Life grant He2190/13-1 / 2018/31/F/NZ1/01856 as well as Polish high-performance computing infrastructure PLGrid (HPC Center: ACK Cyfronet AGH) for providing computer facilities and support within computational grant no. PLG/2023/016888, PLG/2022/016024 and PLG/2021/015218.

Files

Steps to reproduce

The detailed protocols for obtaining the data were provided in the linked papers and their supporting information.

Institutions

Philipps-Universitat Marburg Fachbereich Biologie, Polska Akademia Nauk Instytut Katalizy i Fizykochemii Powierzchni

Categories

Biochemistry, Molecular Modeling, Biocatalysis Kinetics

Funding

Narodowe Centrum Nauki

2018/31/F/NZ1/01856

Deutsche Forschungsgemeinschaft

He2190/13-1

Infrastruktura PL-Grid

PLG/2023/016888

Infrastruktura PL-Grid

PLG/2022/016024

Infrastruktura PL-Grid

PLG/2021/015218

Licence