Molecular mechanism of thiocyanate dehydrogenase at atomic resolution

• Published in: International journal of biological macromolecules 2024-11, Vol.279 (Pt 1), p.135058, Article 135058
• Main Authors: Varfolomeeva, Larisa A., Shipkov, Nikolai S., Dergousova, Natalia I., Boyko, Konstantin M., Khrenova, Maria G., Tikhonova, Tamara V., Popov, Vladimir O.
• Format: Article
• Language: English
• Subjects: active sites; bacteria; catalytic activity; Complexes with inhibitors and substrate analog; Copper-containing enzyme; cyanates; energy; family; mechanism of action; Modelling; nitrogen; oxidoreductases; quantum mechanics; selenium; thiocyanates; thiourea
• ISSN: 0141-8130; 1879-0003; 1879-0003
• DOI: 10.1016/j.ijbiomac.2024.135058

Some sulfur-oxidizing bacteria playing an important role in global geochemical cycles utilize thiocyanate as the sole source of energy and nitrogen. In these bacteria the process of thiocyanate into cyanate conversion is mediated by thiocyanate dehydrogenases — a recently discovered family of copper-containing enzymes with the three‑copper active site unique among the other copper proteins. To get a deeper insight into the structure and molecular mechanism of action of thiocyanate dehydrogenases we isolated, purified, and comprehensively characterized an enzyme from the bacterium Pelomicrobium methylotrophicum. High-resolution crystal structures of the thiocyanate dehydrogenase in the free state and in the complexes with the transition state analog, thiourea, and the closest substrate analog, selenocyanate, unveiled the fine details of molecular events occurring at the enzyme active site. During the reaction thiocyanate dehydrogenase undergoes profound conformational change that affects the position of the constituent copper ions and results in the activation of the attacking water molecule. The structure of the enzyme complex with the selenium atom bridged in-between two copper ions was obtained representing an important transient intermediate. Structures of the complexes with inhibitors supplemented with quantum chemical calculations clarify the role of copper ions and refine molecular mechanism of catalysis by thiocyanate dehydrogenase. [Display omitted] •Thiocyanate dehydrogenases (TcDH) are a new family of copper-containing enzymes.•Structure of the TcDH from P. methylotrophicum was resolved at atomic resolution.•During the catalytic cycle TcDH undergoes profound conformational changes.•High-resolution structural data revealed important enzyme intermediates.•Molecular mechanism of TcDH was formulated and verified.