8BCX

Crystal structure of NrfA-1 from Geobacter metallireducens

8BCX の概要

• エントリーDOI: 10.2210/pdb8bcx/pdb
• 分子名称: Nitrite reductase (cytochrome; ammonia-forming), HEME C, SULFATE ION, ... (4 entities in total)
• 機能のキーワード: nitrite reductase, cytochrome c, dissimilatory nitrate reduction to ammonium (dnra), oxidoreductase
• 由来する生物種: Geobacter metallireducens GS-15
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 234019.46

構造登録者

Denkhaus, L.,Siffert, F.,Einsle, O. (登録日: 2022-10-17, 公開日: 2023-08-30, 最終更新日: 2024-10-16)

主引用文献

Denkhaus, L.,Siffert, F.,Einsle, O.
An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens.
Fems Microbiol.Lett., 370:-, 2023

PubMed Abstract: Dissimilatory nitrate reduction to ammonia (DNRA) is a central pathway in the biogeochemical nitrogen cycle, allowing for the utilization of nitrate or nitrite as terminal electron acceptors. In contrast to the competing denitrification to N2, a major part of the essential nutrient nitrogen in DNRA is retained within the ecosystem and made available as ammonium to serve as a nitrogen source for other organisms. The second step of DNRA is mediated by the pentahaem cytochrome c nitrite reductase NrfA that catalyzes the six-electron reduction of nitrite to ammonium and is widely distributed among bacteria. A recent crystal structure of an NrfA ortholog from Geobacter lovleyi was the first characterized representative of a novel subclass of NrfA enzymes that lacked the canonical Ca2+ ion close to the active site haem 1. Here, we report the structural and functional characterization of NrfA from the closely related G. metallireducens. We established the recombinant production of catalytically active NrfA with its unique, lysine-coordinated active site haem heterologously in Escherichia coli and determined its three-dimensional structure by X-ray crystallography to 1.9 Å resolution. The structure confirmed GmNrfA as a further calcium-independent NrfA protein, and it also shows an altered active site that contained an unprecedented aspartate residue, D80, close to the substrate-binding site. This residue formed part of a loop that also caused a changed arrangement of the conserved substrate/product channel relative to other NrfA proteins and rendered the protein insensitive to the inhibitor sulphate. To elucidate the relevance of D80, we produced and studied the variants D80A and D80N that showed significantly reduced catalytic activity.

PubMed: 37460131
DOI: 10.1093/femsle/fnad068

実験手法

X-RAY DIFFRACTION (1.941 Å)