5Y5J

Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state)

5Y5J の概要

• エントリーDOI: 10.2210/pdb5y5j/pdb
• 分子名称: NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: metal-binding, oxidoreductase
• 由来する生物種: Fusarium oxysporum (Fusarium vascular wilt)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 90258.54

構造登録者

Tosha, T.,Nomura, T.,Nishida, T.,Saeki, N.,Okubayashi, K.,Yamagiwa, R.,Sugahara, M.,Nakane, T.,Yamashita, K.,Hirata, K.,Ueno, G.,Kimura, T.,Hisano, T.,Muramoto, K.,Sawai, H.,Takeda, H.,Mizohata, E.,Yamashita, A.,Kanematsu, Y.,Takano, Y.,Nango, E.,Tanaka, R.,Nureki, O.,Ikemoto, Y.,Murakami, H.,Owada, S.,Tono, K.,Yabashi, M.,Yamamoto, M.,Ago, H.,Iwata, S.,Sugimoto, H.,Shiro, Y.,Kubo, M. (登録日: 2017-08-09, 公開日: 2017-12-06, 最終更新日: 2023-11-22)

主引用文献

Tosha, T.,Nomura, T.,Nishida, T.,Saeki, N.,Okubayashi, K.,Yamagiwa, R.,Sugahara, M.,Nakane, T.,Yamashita, K.,Hirata, K.,Ueno, G.,Kimura, T.,Hisano, T.,Muramoto, K.,Sawai, H.,Takeda, H.,Mizohata, E.,Yamashita, A.,Kanematsu, Y.,Takano, Y.,Nango, E.,Tanaka, R.,Nureki, O.,Shoji, O.,Ikemoto, Y.,Murakami, H.,Owada, S.,Tono, K.,Yabashi, M.,Yamamoto, M.,Ago, H.,Iwata, S.,Sugimoto, H.,Shiro, Y.,Kubo, M.
Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8:1585-1585, 2017

PubMed Abstract: Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe-NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.

PubMed: 29147002
DOI: 10.1038/s41467-017-01702-1

実験手法

X-RAY DIFFRACTION (2 Å)