6ZAW

Damage-free NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography

Summary for 6ZAW

• Entry DOI: 10.2210/pdb6zaw/pdb
• Related PRD ID: PRD_900003
• Descriptor: Copper-containing nitrite reductase, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, SULFATE ION, ... (8 entities in total)
• Functional Keywords: nitrite reductase, copper nitrite reductase, copper-containing nitrite reductase, brnir, br2dnir, product-bound, no-bound, damage-free xfel, oxidoreductase
• Biological source: Bradyrhizobium sp. (strain ORS 375)
• Total number of polymer chains: 1
• Total formula weight: 40654.11

Authors

Rose, S.L.,Antonyuk, S.V.,Sasaki, D.,Yamashita, K.,Hirata, K.,Ueno, G.,Ago, H.,Eady, R.R.,Tosha, T.,Yamamoto, M.,Hasnain, S.S. (deposition date: 2020-06-05, release date: 2021-01-20, Last modification date: 2024-01-24)

Primary citation

Rose, S.L.,Antonyuk, S.V.,Sasaki, D.,Yamashita, K.,Hirata, K.,Ueno, G.,Ago, H.,Eady, R.R.,Tosha, T.,Yamamoto, M.,Hasnain, S.S.
An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7:-, 2021

PubMed Abstract: Copper-containing nitrite reductases (CuNiRs), encoded by gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of Recently, we have identified two copies of genes in several α-proteobacteria of the order Rhizobiales including sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR ( NiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (NiR) and green (NiR) subclasses, NiR, 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.

PubMed: 33523860
DOI: 10.1126/sciadv.abd8523

Experimental method

X-RAY DIFFRACTION (1.3 Å)