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Copper nitrite reductase from Sinorhizobium meliloti 2011: crystal structure and interaction with the physiological vs. a non‐metabolically‐related cupredoxin‐like mediator

DOI: 10.1002/pro.4195 DOI Help

Authors: Cintia Soledad Ramírez (Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria) , Carmien Tolmie (University of the Free State (UFS)) , Diederik Johannes Opperman (University of the Free State (UFS)) , Pablo Javier González (Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria) , María Gabriela Rivas (Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria) , Carlos Dante Brondino (niversidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria) , Felix Martin Ferroni (Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Protein Science

State: Published (Approved)
Published: September 2021
Diamond Proposal Number(s): 15292

Abstract: We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically-related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 å, showed a striking resemblance with the overall structure of the well-known class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.

Journal Keywords: copper; nitrite reductase; NirK; X-ray crystal structure; pseudoazurin; Sinorhizobium meliloti 2011.

Diamond Keywords: Bacteria

Subject Areas: Biology and Bio-materials

Instruments: I04-1-Macromolecular Crystallography (fixed wavelength)

Added On: 27/09/2021 13:37

Discipline Tags:

Life Sciences & Biotech Agriculture & Fisheries Structural biology

Technical Tags:

Diffraction Macromolecular Crystallography (MX)