Electron transfer and docking between cytochrome cd1 nitrite reductase and different redox partners - A comparative...

Area of Science:

• Biochemistry
• Microbiology
• Enzymology

Background:

• Cytochrome cd1 nitrite reductases (cd1NiRs) are key enzymes in denitrification, catalyzing nitrite to nitric oxide conversion.
• Enzymatic activity is linked to electron transfer (ET) through the enzyme's ET domain and heme c center.
• Marinobacter hydrocarbonoclasticus cd1NiR (Mhcd1NiR) is a model enzyme for studying these processes.

Purpose of the Study:

• To investigate the factors influencing the catalytic activity of Mhcd1NiR.
• To determine the role of the electron transfer rate and redox partner specificity in cd1NiR function.
• To elucidate the molecular basis for efficient electron transfer between Mhcd1NiR and its redox partners.

Main Methods:

• Mediated electrochemistry was employed to test Mhcd1NiR activity with various redox partners.
• Small electron transfer proteins and chemical redox mediators were utilized.
• Molecular docking simulations were performed using the 3D model of Mhcd1NiR and its potential redox partners.

Main Results:

• Enzymatic reaction rates varied significantly depending on the redox partner, with cytochrome c552 yielding the highest activity.
• Slower catalytic responses were observed with horse heart cytochrome c and chemical mediators, indicating slower intermolecular ET rates.
• Molecular docking revealed favorable hydrophobic interactions for complex formation, but only cyt c552 allowed for competent ET pathways due to optimal heme-heme distances and contact areas.
• Coupling Mhcd1NiR with chemical redox mediators was energetically unfavorable.

Conclusions:

• Efficient electron transfer and catalytic activity of Mhcd1NiR are highly dependent on the specific redox partner.
• Cytochrome c552 is identified as the likely physiological electron donor for Mhcd1NiR, facilitating efficient intermolecular electron transfer.
• Suboptimal interactions with other redox partners limit the functional complex formation and overall enzyme activity.