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High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase
https://repo.qst.go.jp/records/78964
https://repo.qst.go.jp/records/78964b6b757cb-def2-48f6-a01e-cafc8101511c
| Item type | 学術雑誌論文 / Journal Article(1) | |||||
|---|---|---|---|---|---|---|
| 公開日 | 2020-02-12 | |||||
| タイトル | ||||||
| タイトル | High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
| 資源タイプ | journal article | |||||
| アクセス権 | ||||||
| アクセス権 | metadata only access | |||||
| アクセス権URI | http://purl.org/coar/access_right/c_14cb | |||||
| 著者 |
Fukuda, Yota
× Fukuda, Yota× Hirano, Yuu× Kusaka, Katsuhiro× Inoue, Tsuyoshi× Tamada, Taro× Yuu, Hirano× Taro, Tamada |
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| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide,which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels. |
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| 書誌情報 |
Proceedings of the National Academy of Sciences of the United States of America 巻 117, 号 8, p. 4071-4077, 発行日 2020-02 |
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| 出版者 | ||||||
| 出版者 | National Academy of Sciences | |||||
| ISSN | ||||||
| 収録物識別子タイプ | ISSN | |||||
| 収録物識別子 | 0027-8424 | |||||
| DOI | ||||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | 10.1073/pnas.1918125117 | |||||
| 関連サイト | ||||||
| 識別子タイプ | URI | |||||
| 関連識別子 | https://www.pnas.org/content/early/2020/02/07/1918125117 | |||||
