8Q9Y

The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum in complex with inhibitor thiourea at 1.10 A resolution

Summary for 8Q9Y

• Entry DOI: 10.2210/pdb8q9y/pdb
• Related: 8Q9X
• Descriptor: Twin-arginine translocation signal domain-containing protein, GLYCEROL, THIOUREA, ... (5 entities in total)
• Functional Keywords: thiocyanate dehydrogenase, copper enzyme, trinuclear copper center, atomic resolution, conformational changes, complex with inhibitor, thiourea, pelomicrobium methylotrophicum, oxidoreductase
• Biological source: Pelomicrobium methylotrophicum
• Total number of polymer chains: 2
• Total formula weight: 109018.82

Authors

Varfolomeeva, L.A.,Polyakov, K.M.,Shipkov, N.S.,Dergousova, N.I.,Boyko, K.M.,Tikhonova, T.V.,Popov, V.O. (deposition date: 2023-08-22, release date: 2023-09-13, Last modification date: 2025-05-21)

Primary citation

Varfolomeeva, L.A.,Shipkov, N.S.,Dergousova, N.I.,Boyko, K.M.,Khrenova, M.G.,Tikhonova, T.V.,Popov, V.O.
Molecular mechanism of thiocyanate dehydrogenase at atomic resolution.
Int.J.Biol.Macromol., 279:135058-135058, 2024

PubMed Abstract: 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.

PubMed: 39191340
DOI: 10.1016/j.ijbiomac.2024.135058

Experimental method

X-RAY DIFFRACTION (1.1 Å)