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Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction

DOI: 10.1111/febs.15324 DOI Help

Authors: Daisuke Sasaki (University of Liverpool) , Tatiana F. Watanabe (University of Liverpool; University of São Paulo) , Robert R. Eady (University of Liverpool) , Richard C. Garratt (University of São Paulo) , Svetlana V. Antonyuk (University of Liverpool) , S. Samar Hasnain (University of Liverpool)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: The Febs Journal

State: Published (Approved)
Published: April 2020
Diamond Proposal Number(s): 15991

Open Access Open Access

Abstract: Cu‐containing nitrite reductases that convert NO2‐ to NO are critical enzymes in nitrogen‐based energy metabolism. Among organisms in the order Rhizobiales, we have identified two copies of nirK, one encoding a new class of 4‐domain CuNiR that has both cytochrome and cupredoxin domains fused at the N‐terminus and the other, a classical 2‐domain CuNiR (Br2DNiR). We report the first enzymatic studies of a novel 4‐domain CuNiR from Bradyrhizobium sp. ORS 375 (BrNiR), its genetically engineered 3‐ and 2‐domain variants, and Br2DNiR revealing up to ~500‐fold difference in catalytic efficiency in comparison with classical 2‐domain CuNiRs. Contrary to the expectation that tethering would enhance electron delivery by restricting the conformational search by having a self‐contained donor‐acceptor system, we demonstrate that 4‐domain BrNiR utilises N‐terminal tethering for down‐regulating enzymatic activity instead. Both Br2DNiR, as well as engineered 2‐domain variant of BrNiR (Δ(Cytc‐Cup) BrNiR), have 3 to 5 % NiR activity compared to the well‐characterized 2‐domain CuNiRs from Alcaligenes xylosoxidans (AxNiR) and Achromobacter cycloclastes (AcNiR). Structural comparison of Δ(Cytc‐Cup) BrNiR and Br2DNiR with classical 2‐domain AxNiR and AcNiR reveals structural differences of the proton transfer pathway that could be responsible for the lowering of activity. Our study provides insights into unique structural and functional characteristics of naturally‐occurring 4‐domain CuNiR and its engineered 3‐ and 2‐domain variants.The reverse protein engineering approach utilized here provides has shed light onto the broader question of the evolution of transient encounter complexes and tethered electron transfer complexes.

Journal Keywords: Denitrification; multi‐domain protein; protein‐protein interaction; protein engineering electron transfer; catalysis

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I04-1-Macromolecular Crystallography (fixed wavelength) , I24-Microfocus Macromolecular Crystallography