Intra-electron transfer induced by protonation in copper-containing nitrite reductase

Area of Science:

• Biochemistry
• Enzyme kinetics
• Bioinorganic chemistry

Background:

• Copper-containing nitrite reductase (CuNiR) is vital for nitrogen cycling.
• Understanding electron and proton transfer is key to CuNiR mechanism.
• Previous studies have elucidated parts of the catalytic cycle.

Purpose of the Study:

• To investigate the inter- and intra-electron and proton transfers in CuNiR.
• To model the roles of type 1 (T1) and type 2 (T2) copper sites.
• To elucidate the influence of nitrite binding and protonation on electron transfer.

Main Methods:

• Quantum Mechanics/Molecular Mechanics (QM/MM) method.
• Computational modeling of CuNiR with T1 and T2 Cu sites.
• Analysis of electron and proton transfer pathways.

Main Results:

• Electron transfer to T1 Cu occurs before and after nitrite binding; binding lowers T1 reduction potential.
• Protonation of His244 and T1 Cu reduction trigger T1 to T2 Cu electron transfer.
• Proton transfer from His244 to nitrite via hydrogen bonds drives T1 to T2 Cu electron transfer.
• T1 Cu ligand interactions and water molecules in the proton pool modulate T1 reduction potential and His244 basicity.
• Nitrite binding alters the water network around the sensor loop without changing its conformation.

Conclusions:

• The study details the intricate electron and proton transfer steps in CuNiR catalysis.
• Nitrite binding and protonation are critical regulatory events.
• The proton pool and sensor loop water network play significant roles in enzyme function.