2DWS

Cu-containing nitrite reductase at pH 8.4 with bound nitrite

Summary for 2DWS

• Entry DOI: 10.2210/pdb2dws/pdb
• Related: 1ZV2 2DWT 2DY2
• Descriptor: Copper-containing nitrite reductase, COPPER (II) ION, NITRITE ION, ... (4 entities in total)
• Functional Keywords: copper protein, cupredoxin, denitrification, oxidoreductase
• Biological source: Rhodobacter sphaeroides
• Cellular location: Periplasm : Q53239
• Total number of polymer chains: 1
• Total formula weight: 35971.58

Authors

Jacobson, F. (deposition date: 2006-08-16, release date: 2006-12-05, Last modification date: 2023-10-25)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.85 Å)