6THF

Crystal structure of two-domain Cu nitrite reductase from Bradyrhizobium sp. ORS 375

6THF の概要

• エントリーDOI: 10.2210/pdb6thf/pdb
• 分子名称: Copper-containing nitrite reductase, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: two-domain, copper-containing nitrite reductase, bradyrhizobium sp. ors 375, electron transfer, oxidoreductase
• 由来する生物種: Bradyrhizobium sp. ORS 375
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 39373.07

構造登録者

Sasaki, D.,Watanabe, T.F.,Eady, R.R.,Garratt, R.C.,Antonyuk, S.V.,Hasnain, S.S. (登録日: 2019-11-20, 公開日: 2020-04-22, 最終更新日: 2024-01-24)

主引用文献

Sasaki, D.,Watanabe, T.F.,Eady, R.R.,Garratt, R.C.,Antonyuk, S.V.,Hasnain, S.S.
Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction.
Febs J., 288:262-280, 2021

PubMed Abstract: Cu-containing nitrite reductases that convert NO 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 (Br NiR). 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 Br NiR 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 utilizes N-terminal tethering for downregulating enzymatic activity instead. Both Br NiR and an 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 Br NiR 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 has shed light onto the broader question of the evolution of transient encounter complexes and tethered electron transfer complexes. ENZYME: Copper-containing nitrite reductase (CuNiR) (EC 1.7.2.1). DATABASE: The atomic coordinate and structure factor of Δ(Cytc-Cup) BrNiR and Br NiR have been deposited in the Protein Data Bank (http://www.rcsb.org/) under the accession code 6THE and 6THF, respectively.

PubMed: 32255260
DOI: 10.1111/febs.15324

実験手法

X-RAY DIFFRACTION (1.47 Å)