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An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures

DOI: 10.1126/sciadv.abd8523 DOI Help

Authors: Samuel L. Rose (University of Liverpool) , Svetlana V. Antonyuk (University of Liverpool) , Daisuke Sasaki (University of Liverpool) , Keitaro Yamashita (The University of Tokyo) , Kunio Hirata (RIKEN SPring-8 Center) , Go Ueno (RIKEN SPring-8 Center) , Hideo Ago (RIKEN SPring-8 Center) , Robert R. Eady (University of Liverpool) , Takehiko Tosha (RIKEN SPring-8 Center) , Masaki Yamamoto (RIKEN SPring-8 Center) , S. Samar Hasnain (University of Liverpool)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Science Advances , VOL 7

State: Published (Approved)
Published: January 2021
Diamond Proposal Number(s): 15991

Open Access Open Access

Abstract: Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK. Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br2DNiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.

Subject Areas: Chemistry, Biology and Bio-materials

Instruments: I03-Macromolecular Crystallography

Other Facilities: BL41XU at SPring-8