6KNG

CryoEM map and model of Nitrite Reductase at pH 8.1

6KNG の概要

• エントリーDOI: 10.2210/pdb6kng/pdb
• EMDBエントリー: 0731
• 分子名称: Copper-containing nitrite reductase, COPPER (II) ION (2 entities in total)
• 機能のキーワード: cu containing nitrite reductase, oxidoreductase
• 由来する生物種: Achromobacter cycloclastes
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 110245.27

構造登録者

Adachi, N.,Yamaguchi, T.,Moriya, T.,Kawasaki, M.,Koiwai, K.,Shinoda, A.,Yamada, Y.,Yumoto, F.,Kohzuma, T.,Senda, T. (登録日: 2019-08-05, 公開日: 2020-08-12, 最終更新日: 2024-05-29)

主引用文献

Adachi, N.,Yamaguchi, T.,Moriya, T.,Kawasaki, M.,Koiwai, K.,Shinoda, A.,Yamada, Y.,Yumoto, F.,Kohzuma, T.,Senda, T.
2.85 and 2.99 angstrom resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.
J.Struct.Biol., 213:107768-107768, 2021

PubMed Abstract: Cu-containing nitrite reductases (NiRs) are 110 kDa enzymes that play central roles in denitrification. Although the NiRs have been well studied, with over 100 Protein Data Bank entries, such issues as crystal packing, photoreduction, and lack of high pH cases have impeded structural analysis of their catalytic mechanisms. Here we show the cryogenic electron microscopy (cryo-EM) structures of Achromobacter cycloclastes NiR (AcNiR) at pH 6.2 and 8.1. The optimization of 3D-reconstruction parameters achieved 2.99 and 2.85 Å resolution. Comprehensive comparisons with cryo-EM and 56 AcNiR crystal structures suggested crystallographic artifacts in residues 185-215 and His255' due to packing and photoreduction, respectively. We used a newly developed map comparison method to detect structural change around the type 2 Cu site. While the theoretical estimation of coordinate errors of cryo-EM structures remains difficult, combined analysis using X-ray and cryo-EM structures will allow deeper insight into the local structural changes of proteins.

PubMed: 34217801
DOI: 10.1016/j.jsb.2021.107768

実験手法

ELECTRON MICROSCOPY (2.85 Å)