6L46

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

Summary for 6L46

• Entry DOI: 10.2210/pdb6l46/pdb
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, SODIUM ION, ... (6 entities in total)
• Functional Keywords: copper, nitrite reductase, neutron, oxidoreductase
• Biological source: Geobacillus thermodenitrificans
• Total number of polymer chains: 1
• Total formula weight: 35953.86

Authors

Fukuda, Y.,Hirano, Y.,Kusaka, K.,Inoue, T.,Tamada, T. (deposition date: 2019-10-16, release date: 2020-02-12, Last modification date: 2024-04-03)

Primary citation

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

Experimental method

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