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![Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase](/_next/image?url=https%3A%2F%2Fcloudfront.jove.com%2FCDNSource%2Fteasers%2F55858.jpg&w=3840&q=50)
Protein Film Infrared Electrochemistry Demonstrated for Study of H2 Oxidation by a [NiFe] Hydrogenase
Published on: December 4, 2017
Structural insights into the function of a thermostable copper-containing nitrite reductase
Yohta Fukuda1, Ka Man Tse, Masami Lintuluoto
1Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Applied Chemistry, School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Faculty of Life and Environmental Sciences, Department of Environmental Information, Kyoto Prefectural University, Shimogamo-Hanki-cho, Sakyou, Kyoto 606-8522, Japan; Molecular-Recognition Structure Analysis Team, Molecular Profiling Research Center for Drug Discovery (molprof) National Institute of Advanced Industrial Science and Technology (AIST) 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan; Microbial Genome Research Group, Japan Agency of Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan; and RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
The crystal structure of Geobacillus thermodenitrificans nitrite reductase (GtNIR) reveals a novel nitrite binding mode. This finding provides insights into the catalytic mechanism of copper-containing nitrite reductases during denitrification.
Area of Science:
- Biochemistry
- Structural Biology
- Microbiology
Background:
- Copper-containing nitrite reductase (CuNIR) is crucial for denitrification, catalyzing nitrite reduction to nitric oxide.
- Understanding the structure-function relationship of CuNIR is essential for elucidating microbial respiration pathways.
Purpose of the Study:
- To determine the high-resolution crystal structures of CuNIR from Geobacillus thermodenitrificans (GtNIR).
- To elucidate the catalytic mechanism of GtNIR, particularly the nitrite binding mode at the T2Cu site.
Main Methods:
- X-ray crystallography was used to determine the structures of wild-type GtNIR and a C135A mutant.
- High-resolution structures (1.15 Å and 1.90 Å) were obtained for different ligand-bound forms.
Main Results:
- A unique η(1)-O coordination mode of nitrite at the T2Cu site was observed in the C135A mutant structure.
- Steric restrictions imposed by Phe109 and an unusual hydrogen bond involving His244 limit the mobility of key catalytic residues.
- Comparison with WT structures suggests a proton flow path and a revised catalytic mechanism.
Conclusions:
- The study proposes a novel reaction mechanism for GtNIR involving the η(1)-O nitrite coordination.
- Structural insights into GtNIR advance our understanding of denitrification enzymes and their catalytic strategies.
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