8YOU

The pmTcDH complex structure with an inhibitor SeCN

8YOU の概要

• エントリーDOI: 10.2210/pdb8you/pdb
• 分子名称: Twin-arginine translocation signal domain-containing protein, SELENOCYANATE ION, COPPER (II) ION, ... (7 entities in total)
• 機能のキーワード: thiocyanate dehydrogenase, pelomicrobium methylotrophicum, substrate analogue, inhibitor, complex, tcdh, trinuclear copper center, selenocyanate, secn, oxidoreductase
• 由来する生物種: Pelomicrobium methylotrophicum
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 108930.45

構造登録者

Varfolomeeva, L.A.,Polyakov, K.M.,Shipkov, N.S.,Dergousova, N.I.,Boyko, K.M.,Tikhonova, T.V.,Popov, V.O. (登録日: 2024-03-13, 公開日: 2024-03-27, 最終更新日: 2025-05-21)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.8 Å)