6ZAV
NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 A resolution (unrestrained, full matrix refinement by SHELX)
Summary for 6ZAV
| Entry DOI | 10.2210/pdb6zav/pdb |
| Related PRD ID | PRD_900003 |
| Descriptor | Copper-containing nitrite reductase, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, COPPER (II) ION, ... (7 entities in total) |
| Functional Keywords | nitrite reductase, copper nitrite reductase, copper-containing nitrite reductase, brnir, br2dnir, no-bound, product-bound, oxidoreductase, atomic resolution |
| Biological source | Bradyrhizobium sp. (strain ORS 375) |
| Total number of polymer chains | 1 |
| Total formula weight | 40710.11 |
| 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 Cited by 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: 33523860DOI: 10.1126/sciadv.abd8523 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.19 Å) |
Structure validation
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