6L46

High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans

6L46 の概要

• エントリーDOI: 10.2210/pdb6l46/pdb
• 分子名称: Copper-containing nitrite reductase, COPPER (II) ION, SODIUM ION, ... (6 entities in total)
• 機能のキーワード: copper, nitrite reductase, neutron, oxidoreductase
• 由来する生物種: Geobacillus thermodenitrificans
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 35953.86

構造登録者

Fukuda, Y.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. (登録日: 2019-10-16, 公開日: 2020-02-12, 最終更新日: 2024-04-03)

主引用文献

Fukuda, Y.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T.
High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase.
Proc.Natl.Acad.Sci.USA, 117:4071-4077, 2020

PubMed Abstract: 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 (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.

PubMed: 32041886
DOI: 10.1073/pnas.1918125117

実験手法

NEUTRON DIFFRACTION (1.5 Å)
X-RAY DIFFRACTION (1.3 Å)