5Y5G

Structure of cytochrome P450nor in NO-bound state: damaged by high-dose (5.7 MGy) X-ray

Summary for 5Y5G

• Entry DOI: 10.2210/pdb5y5g/pdb
• Descriptor: NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ... (5 entities in total)
• Functional Keywords: metal-binding, oxidoreductase
• Biological source: Fusarium oxysporum (Fusarium vascular wilt)
• Total number of polymer chains: 1
• Total formula weight: 45159.28

Authors

Tosha, T.,Nomura, T.,Nishida, T.,Ueno, G.,Murakami, H.,Yamashita, K.,Hirata, K.,Yamamoto, M.,Ago, H.,Sugimoto, H.,Shiro, Y.,Kubo, M. (deposition date: 2017-08-09, release date: 2017-12-06, Last modification date: 2023-11-22)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.36 Å)