7ZCO

Nitrite-bound MSOX movie series dataset 8 (6.4 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - nitrite/NO intermediate

Summary for 7ZCO

• Entry DOI: 10.2210/pdb7zco/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, nitrite-bound, msox, oxidoreductase
• Biological source: Bradyrhizobium sp. ORS 375
• Total number of polymer chains: 1
• Total formula weight: 40646.86

Authors

Rose, S.L.,Baba, S.,Okumura, H.,Antonyuk, S.V.,Sasaki, D.,Tosha, T.,Kumasaka, T.,Eady, R.R.,Yamamoto, M.,Hasnain, S.S. (deposition date: 2022-03-28, release date: 2022-08-03, Last modification date: 2024-01-31)

Primary citation

Rose, S.L.,Baba, S.,Okumura, H.,Antonyuk, S.V.,Sasaki, D.,Hedison, T.M.,Shanmugam, M.,Heyes, D.J.,Scrutton, N.S.,Kumasaka, T.,Tosha, T.,Eady, R.R.,Yamamoto, M.,Hasnain, S.S.
Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases.
Proc.Natl.Acad.Sci.USA, 119:e2205664119-e2205664119, 2022

PubMed Abstract: Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a species (NiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.

PubMed: 35862453
DOI: 10.1073/pnas.2205664119

Experimental method

X-RAY DIFFRACTION (1.22 Å)