Structures of a blue-copper nitrite reductase and its substrate-bound complex

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Copper-containing nitrite reductases (NiRs) are classified as blue or green types.
• Blue NiRs are redox partners of azurins, while green NiRs partner with pseudo-azurins.
• The crystal structures of two green NiRs are known; this study focuses on a blue NiR from Alcaligenes xylosoxidans (AxNiR).

Purpose of the Study:

• To present the first crystal structure of a blue copper nitrite reductase (AxNiR) in its oxidized and nitrite-bound forms.
• To investigate the copper sites within AxNiR and their interaction with nitrite.
• To elucidate the structural basis for color differences in blue copper centers and the enzyme mechanism.

Main Methods:

• X-ray crystallography was used to determine the structure of AxNiR.
• The structures were analyzed in both oxidized and nitrite-bound states.
• Comparison with existing structural data of other copper proteins and mutants was performed.

Main Results:

• The crystal structure of AxNiR reveals the copper sites, including the copper-sulfur (met) distance, which is similar to green NiRs.
• Nitrite binds to the catalytic copper in a bidentate manner, displacing a water molecule.
• The displacement of copper from its ligand plane is proposed as the cause for color variation in blue copper centers.

Conclusions:

• The Cu-Smet bond length does not explain the color differences between blue and green NiRs.
• Nitrite binding induces structural changes at the type-2 copper site, increasing coordination and rationalizing XAFS observations.
• Structural insights into AxNiR provide a mechanistic understanding of nitrite reduction by blue copper enzymes.