2DWS

Cu-containing nitrite reductase at pH 8.4 with bound nitrite

2DWS の概要

• エントリーDOI: 10.2210/pdb2dws/pdb
• 関連するPDBエントリー: 1ZV2 2DWT 2DY2
• 分子名称: Copper-containing nitrite reductase, COPPER (II) ION, NITRITE ION, ... (4 entities in total)
• 機能のキーワード: copper protein, cupredoxin, denitrification, oxidoreductase
• 由来する生物種: Rhodobacter sphaeroides
• 細胞内の位置: Periplasm : Q53239
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 35971.58

構造登録者

Jacobson, F. (登録日: 2006-08-16, 公開日: 2006-12-05, 最終更新日: 2023-10-25)

主引用文献

Jacobson, F.,Pistorius, A.,Farkas, D.,De Grip, W.,Hansson, O.,Sjolin, L.,Neutze, R.
pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase
J.Biol.Chem., 282:6347-6355, 2007

PubMed Abstract: Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.

PubMed: 17148448
DOI: 10.1074/jbc.M605746200

実験手法

X-RAY DIFFRACTION (1.85 Å)