8RFL

Low pH (5.5) nitrite-bound MSOX movie series dataset 1 of the copper nitrite reductase (NirK) from Bradyrhizobium japonicum USDA110 [0.61 MGy] - nitrite (start)

Summary for 8RFL

• Entry DOI: 10.2210/pdb8rfl/pdb
• Related PRD ID: PRD_900003
• Descriptor: Copper-containing nitrite reductase, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, COPPER (II) ION, ... (6 entities in total)
• Functional Keywords: copper nitrite reductase, copper-containing nitrite reductase, brjnir, low ph, nitrite-bound, msox, oxidoreductase
• Biological source: Bradyrhizobium diazoefficiens USDA 110
• Total number of polymer chains: 1
• Total formula weight: 38285.93

Authors

Rose, S.L.,Ferroni, F.M.,Antonyuk, S.V.,Eady, R.R.,Hasnain, S.S. (deposition date: 2023-12-13, release date: 2024-07-24, Last modification date: 2024-08-07)

Primary citation

Rose, S.L.,Ferroni, F.M.,Horrell, S.,Brondino, C.D.,Eady, R.R.,Jaho, S.,Hough, M.A.,Owen, R.L.,Antonyuk, S.V.,Hasnain, S.S.
Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases.
J.Mol.Biol., 436:168706-168706, 2024

PubMed Abstract: Copper nitrite reductases (CuNiRs) exhibit a strong pH dependence of their catalytic activity. Structural movies can be obtained by serially recording multiple structures (frames) from the same spot of a crystal using the MSOX serial crystallography approach. This method has been combined with on-line single crystal optical spectroscopy to capture the pH-dependent structural changes that accompany during turnover of CuNiRs from two Rhizobia species. The structural movies, initiated by the redox activation of a type-1 copper site (T1Cu) via X-ray generated photoelectrons, have been obtained for the substrate-free and substrate-bound states at low (high enzymatic activity) and high (low enzymatic activity) pH. At low pH, formation of the product nitric oxide (NO) is complete at the catalytic type-2 copper site (T2Cu) after a dose of 3 MGy (frame 5) with full bleaching of the T1Cu ligand-to-metal charge transfer (LMCT) 455 nm band (S(σ) → T1Cu) which in itself indicates the electronic route of proton-coupled electron transfer (PCET) from T1Cu to T2Cu. In contrast at high pH, the changes in optical spectra are relatively small and the formation of NO is only observed in later frames (frame 15 in BrNiR, 10 MGy), consistent with the loss of PCET required for catalysis. This is accompanied by decarboxylation of the catalytic Asp residue, with CO trapped in the catalytic pocket.

PubMed: 39002715
DOI: 10.1016/j.jmb.2024.168706

Experimental method

X-RAY DIFFRACTION (1.16 Å)