Download MendeleyQuantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA.
Degtjarik, O., Brynda, J., Ettrichova, O., Kuty, M., Sinha, D., Kuta Smatanova, I., Carey, J., Ettrich, R., Reha, D.(2016) J Phys Chem B 120: 4867-4877
- PubMed: 27183467
- DOI: https://doi.org/10.1021/acs.jpcb.5b11958
- Primary Citation of Related Structures:
4YQE, 5F12 - PubMed Abstract:
Quantum mechanical calculations using the Marcus equation are applied to compare the electron-transfer probability for two distinct crystal structures of the Escherichia coli protein WrbA, an FMN-dependent quinone oxidoreductase, with the bound substrate benzoquinone. The calculations indicate that the position of benzoquinone in a new structure reported here and solved at 1.33 Å resolution is more likely to be relevant for the physiological reaction of WrbA than a previously reported crystal structure in which benzoquinone is shifted by ∼5 Å. Because the true electron-acceptor substrate for WrbA is not yet known, the present results can serve to constrain computational docking attempts with potential substrates that may aid in identifying the natural substrate(s) and physiological role(s) of this enzyme. The approach used here highlights a role for quantum mechanical calculations in the interpretation of protein crystal structures.
Organizational Affiliation:
Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
