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 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: 29147002DOI: 10.1038/s41467-017-01702-1 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.36 Å) |
Structure validation
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