Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin‐like mediator

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.

Biochemical Characterization of the Copper Nitrite Reductase from Neisseria gonorrhoeae

“…Comparison of the dihedral angles between the His 1 -Cu-His 2 and Cys-Cu-Met planes of CuNiRs ( Table S1 in the Supplementary Materials ) shows that the T1Cu center of Ng CuNiR has the smaller angle, indicating a more distorted center. Since discrepancies between these values have been reported between damage-prone and damage-free structures [ 62 ], these differences and their contribution to the electronic properties of the T1Cu center need to be re-analyzed, as suggested by C. Brondino in [ 63 ].…”