Loading
PDBj
メニューPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

5Y5F

Structure of cytochrome P450nor in NO-bound state: damaged by low-dose (0.72 MGy) X-ray

5Y5F の概要
エントリーDOI10.2210/pdb5y5f/pdb
分子名称NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ... (5 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1
化学式量合計45159.28
構造登録者
Tosha, T.,Nomura, T.,Nishida, T.,Ueno, G.,Murakami, H.,Yamashita, K.,Hirata, K.,Yamamoto, M.,Ago, H.,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
Cited by
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
主引用文献が同じPDBエントリー
実験手法
X-RAY DIFFRACTION (1.5 Å)
構造検証レポート
Validation report summary of 5y5f
検証レポート(詳細版)ダウンロードをダウンロード

226707

件を2024-10-30に公開中

PDB statisticsPDBj update infoContact PDBjnumon