3D1I

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite

3D1I の概要

• エントリーDOI: 10.2210/pdb3d1i/pdb
• 関連するPDBエントリー: 2OT4 2ZO5
• 分子名称: Eight-heme nitrite reductase, HEME C, CALCIUM ION, ... (8 entities in total)
• 機能のキーワード: cytochrome c nitrite reductase, nrfa, sulfite reductase, oxidoreductase
• 由来する生物種: Thioalkalivibrio nitratireducens
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 130874.99

構造登録者

Polyakov, K.M.,Boyko, K.M.,Slutsky, A.,Tikhonova, T.V.,Antipov, A.N.,Zvyagilskaya, R.A.,Popov, A.N.,Lamzin, V.S.,Bourenkov, G.P.,Popov, V.O. (登録日: 2008-05-06, 公開日: 2009-05-12, 最終更新日: 2023-11-01)

主引用文献

Polyakov, K.M.,Boyko, K.M.,Tikhonova, T.V.,Slutsky, A.,Antipov, A.N.,Zvyagilskaya, R.A.,Popov, A.N.,Bourenkov, G.P.,Lamzin, V.S.,Popov, V.O.
High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens
J.Mol.Biol., 389:846-862, 2009

PubMed Abstract: Bacterial pentaheme cytochrome c nitrite reductases (NrfAs) are key enzymes involved in the terminal step of dissimilatory nitrite reduction of the nitrogen cycle. Their structure and functions are well studied. Recently, a novel octaheme cytochrome c nitrite reductase (TvNiR) has been isolated from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. Here we present high-resolution crystal structures of the apoenzyme and its complexes with the substrate (nitrite) and the inhibitor (azide). Both in the crystalline state and in solution, TvNiR exists as a stable hexamer containing 48 hemes-the largest number of hemes accommodated within one protein molecule known to date. The subunit of TvNiR consists of two domains. The N-terminal domain has a unique fold and contains three hemes. The catalytic C-terminal domain hosts the remaining five hemes, their arrangement, including the catalytic heme, being identical to that found in NrfAs. The complete set of eight hemes forms a spatial pattern characteristic of other multiheme proteins, including structurally characterized octaheme cytochromes. The catalytic machinery of TvNiR resembles that of NrfAs. It comprises the lysine residue at the proximal position of the catalytic heme, the catalytic triad of tyrosine, histidine, and arginine at the distal side, channels for the substrate and product transport with a characteristic gradient of electrostatic potential, and, finally, two conserved Ca(2+)-binding sites. However, TvNiR has a number of special structural features, including a covalent bond between the catalytic tyrosine and the adjacent cysteine and the unusual topography of the product channels that open into the void interior space of the protein hexamer. The role of these characteristic structural features in the catalysis by this enzyme is discussed.

PubMed: 19393666
DOI: 10.1016/j.jmb.2009.04.037

実験手法

X-RAY DIFFRACTION (1.8 Å)