4YSP

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 8.32 MGy

4YSP の概要

• エントリーDOI: 10.2210/pdb4ysp/pdb
• 関連するPDBエントリー: 4YSA 4YSC 4YSD 4YSE 4YSO 4YSQ 4YSR 4YSS 4YST 4YSU
• 分子名称: Nitrite reductase, COPPER (II) ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total)
• 機能のキーワード: nitrite, copper, reductase, oxidoreductase
• 由来する生物種: Geobacillus thermodenitrificans (strain NG80-2)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36182.12

構造登録者

Fukuda, Y.,Tse, K.M.,Suzuki, M.,Diedrichs, K.,Hirata, K.,Nakane, T.,Sugahara, M.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Song, C.,Hatsui, T.,Yabashi, M.,Nureki, O.,Matsumura, H.,Inoue, T.,Iwata, S.,Mizohata, E. (登録日: 2015-03-17, 公開日: 2016-02-24, 最終更新日: 2024-03-20)

主引用文献

Fukuda, Y.,Tse, K.M.,Suzuki, M.,Diederichs, K.,Hirata, K.,Nakane, T.,Sugahara, M.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Song, C.,Hatsui, T.,Yabashi, M.,Nureki, O.,Matsumura, H.,Inoue, T.,Iwata, S.,Mizohata, E.
Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography
J.Biochem., 159:527-538, 2016

PubMed Abstract: Serial femtosecond crystallography (SFX) has enabled the damage-free structural determination of metalloenzymes and filled the gaps of our knowledge between crystallographic and spectroscopic data. Crystallographers, however, scarcely know whether the rising technique provides truly new structural insights into mechanisms of metalloenzymes partly because of limited resolutions. Copper nitrite reductase (CuNiR), which converts nitrite to nitric oxide in denitrification, has been extensively studied by synchrotron radiation crystallography (SRX). Although catalytic Cu (Type 2 copper (T2Cu)) of CuNiR had been suspected to tolerate X-ray photoreduction, we here showed that T2Cu in the form free of nitrite is reduced and changes its coordination structure in SRX. Moreover, we determined the completely oxidized CuNiR structure at 1.43 Å resolution with SFX. Comparison between the high-resolution SFX and SRX data revealed the subtle structural change of a catalytic His residue by X-ray photoreduction. This finding, which SRX has failed to uncover, provides new insight into the reaction mechanism of CuNiR.

PubMed: 26769972
DOI: 10.1093/jb/mvv133

実験手法

X-RAY DIFFRACTION (1.34 Å)