Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450

Andrei Gilep; Tatsiana Varaksa; Sergey Bukhdruker; Anton Kavaleuski; Yury Ryzhykau; Sviatlana Smolskaya; Tatsiana Sushko; Kouhei Tsumoto; Irina Grabovec; Ivan Kapranov; Ivan Okhrimenko; Egor Marin; Mikhail Shevtsov; Alexey Mishin; Kirill Kovalev; Alexander Kuklin; Valentin Gordeliy; Leonid Kaluzhskiy; Oksana Gnedenko; Evgeniy Yablokov; Alexis Ivanov; Valentin Borshchevskiy; Natallia Strushkevich

doi:10.3389/fmolb.2022.1100032

Structural insights into 3Fe-4S ferredoxins diversity in M. tuberculosis highlighted by a first redox complex with P450

Front Mol Biosci. 2023 Jan 9:9:1100032. doi: 10.3389/fmolb.2022.1100032. eCollection 2022.

Authors

Andrei Gilep^{1

2}, Tatsiana Varaksa¹, Sergey Bukhdruker³, Anton Kavaleuski¹, Yury Ryzhykau^{3

4}, Sviatlana Smolskaya¹, Tatsiana Sushko⁵, Kouhei Tsumoto^{5

6}, Irina Grabovec¹, Ivan Kapranov³, Ivan Okhrimenko³, Egor Marin³, Mikhail Shevtsov³, Alexey Mishin³, Kirill Kovalev⁷, Alexander Kuklin^{3

4}, Valentin Gordeliy⁸, Leonid Kaluzhskiy², Oksana Gnedenko², Evgeniy Yablokov², Alexis Ivanov², Valentin Borshchevskiy^{3

4}, Natallia Strushkevich⁹

Affiliations

¹ Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus.
² Laboratory of Intermolecular Interactions, Institute of Biomedical Chemistry, Moscow, Russia.
³ Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
⁴ Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia.
⁵ Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
⁶ Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
⁷ European Molecular Biology Laboratory, Hamburg Unit C/O DESY, Hamburg, Germany.
⁸ Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.
⁹ Skolkovo Institute of Science and Technology, Moscow, Russia.

Abstract

Ferredoxins are small iron-sulfur proteins and key players in essential metabolic pathways. Among all types, 3Fe-4S ferredoxins are less studied mostly due to anaerobic requirements. Their complexes with cytochrome P450 redox partners have not been structurally characterized. In the present work, we solved the structures of both 3Fe-4S ferredoxins from M. tuberculosis-Fdx alone and the fusion FdxE-CYP143. Our SPR analysis demonstrated a high-affinity binding of FdxE to CYP143. According to SAXS data, the same complex is present in solution. The structure reveals extended multipoint interactions and the shape/charge complementarity of redox partners. Furthermore, FdxE binding induced conformational changes in CYP143 as evident from the solved CYP143 structure alone. The comparison of FdxE-CYP143 and modeled Fdx-CYP51 complexes further revealed the specificity of ferredoxins. Our results illuminate the diversity of electron transfer complexes for the production of different secondary metabolites.

Keywords: 3Fe–4S ferredoxins; crystal structure; cytochrome P450; protein–protein interactions; redox complex.

Copyright © 2023 Gilep, Varaksa, Bukhdruker, Kavaleuski, Ryzhykau, Smolskaya, Sushko, Tsumoto, Grabovec, Kapranov, Okhrimenko, Marin, Shevtsov, Mishin, Kovalev, Kuklin, Gordeliy, Kaluzhskiy, Gnedenko, Yablokov, Ivanov, Borshchevskiy and Strushkevich.

Grants and funding

The SPR analysis was conducted within the framework of the Program for Basic Research in the Russian Federation for a long-term period (2021–2030) (No. 122030100168-2) using the equipment of the “Human Proteome” Core Facility of the Institute of Biomedical Chemistry. Synchrotron data collection and data treatment were supported by the Russian Ministry of Science and Higher Education (Grant No. 075-15-2021-1354).