7P2F

Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011

7P2F の概要

• エントリーDOI: 10.2210/pdb7p2f/pdb
• 分子名称: Copper-containing nitrite reductase, COPPER (II) ION (3 entities in total)
• 機能のキーワード: nitrite reductase, denitrification pathway, greek key b-barrel domains, metal binding protein
• 由来する生物種: Sinorhizobium meliloti 2011
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 121288.36

構造登録者

Tolmie, C.,Opperman, D.J.,Ferroni, F.M. (登録日: 2021-07-05, 公開日: 2021-10-13, 最終更新日: 2024-01-31)

主引用文献

Ramirez, C.S.,Tolmie, C.,Opperman, D.J.,Gonzalez, P.J.,Rivas, M.G.,Brondino, C.D.,Ferroni, F.M.
Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator.
Protein Sci., 30:2310-2323, 2021

PubMed 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.

PubMed: 34562300
DOI: 10.1002/pro.4195

実験手法

X-RAY DIFFRACTION (2.5 Å)