Structural changes of the trinuclear copper center in bilirubin oxidase upon reduction

Takaki Tokiwa, Mitsuo Shoji, Vladimir Sladek, Naoki Shibata, Yoshiki Higuchi, Kunishige Kataoka, Takeshi Sakurai, Yasuteru Shigeta, Fuminori Misaizu

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1 Citation (Scopus)

Abstract

Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted density functional theory (UDFT) method was adopted for the open-shell system. We found new candidates of the native intermediate (NI, intermediate II) and the resting oxidized (RO) states, i.e., NIH+ and RO0. Elongations of the Cu-Cu atomic distances for the trinuclear Cu center (TNC) and very small structural changes around the type I Cu (T1Cu) were calculated as the results of a four-electron reduction. The QM/MM optimized structures are in good agreement with recent high-resolution X-ray structures. As the structural change in the TNC upon reduction was revealed to be the change in the size of the triangle spanned by the three Cu atoms of TNC, we introduced a new index (l) to characterize the specific structural change. Not only the wild-type, but also the M467Q, which mutates the amino acid residue coordinating T1Cu, were precisely analyzed in terms of their molecular orbital levels, and the optimized redox potential of T1Cu was theoretically reconfirmed.

Original languageEnglish
Article number24010076
JournalMolecules
Volume24
Issue number1
DOIs
Publication statusPublished - 2019 Jan 1

Keywords

  • Catalytic intermediate
  • Cu oxidation state
  • Molecular orbital analysis
  • Protonation
  • SONO
  • X-ray reduction

ASJC Scopus subject areas

  • Analytical Chemistry
  • Chemistry (miscellaneous)
  • Molecular Medicine
  • Pharmaceutical Science
  • Drug Discovery
  • Physical and Theoretical Chemistry
  • Organic Chemistry

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  • Cite this

    Tokiwa, T., Shoji, M., Sladek, V., Shibata, N., Higuchi, Y., Kataoka, K., Sakurai, T., Shigeta, Y., & Misaizu, F. (2019). Structural changes of the trinuclear copper center in bilirubin oxidase upon reduction. Molecules, 24(1), [24010076]. https://doi.org/10.3390/molecules24010076