Journal of Molecular Modeling

, Volume 16, Issue 11, pp 1673–1677 | Cite as

On the observation of a gem diol intermediate after O–O bond cleavage by extradiol dioxygenases. A hybrid DFT study

  • Tomasz BorowskiEmail author
  • Valentin Georgiev
  • Per E. M. Siegbahn
Original Paper


Catalytic cycle intermediates of a representative extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase (HPCD), have recently been characterized in crystallo by Kovaleva and Lipscomb. The structures of the identified species indicate that the process of inserting oxygen into the catechol ring occurs stepwise, and involves an Fe(II)-alkylperoxo intermediate and its O–O cleavage product: a gem diol species. In general, these findings corroborate the results of our previous computational studies; however, the fact that the gem diol species is stable enough to be observed in the crystal form seems to be at odds with the computational mechanistic data, which suggest that this intermediate should very readily and spontaneously convert to the epoxide species. The key question then becomes what is actually observed in the X-ray experiments. Here we report additional computational studies undertaken with the hope of clarifying this issue. The results obtained for active site models hosting both the native and the alternative (4-sulfonylcatechol) substrate indicate that the stability of the gem diol species is substantially increased if an electron and a proton are added. If this occurs somehow, the lifetime of the intermediate should be sufficient to observe it.


Homoprotocatechuate 2,3-dioxygenase Extradiol Ring cleavage Density functional calculations 



We are grateful to Sven de Marothy for providing us with his XYZ-Viewer program, which was used to produce Fig. 3. T.B. acknowledges support from the Polish State Committee for Scientific Research (Grant N301 093036).

Supplementary material

894_2010_652_MOESM1_ESM.pdf (114 kb)
(PDF 114 kb)


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Tomasz Borowski
    • 1
    Email author
  • Valentin Georgiev
    • 2
  • Per E. M. Siegbahn
    • 2
  1. 1.Institute of Catalysis and Surface Chemistry, Polish Academy of SciencesCracowPoland
  2. 2.Department of Physics, Stockholm Center for Physics, Astronomy and BiotechnologyStockholm UniversityStockholmSweden

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