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

The inter- and intra-electron and proton transfers in the nitrite reduction of copper-containing nitrite reductase (CuNiR) were investigated by using the QM/MM method with the calculational models containing type 1 (T1) and type 2 (T2) Cu sites. The electron transfer from the outer electron donor protein to the T1 Cu site occurred both before and after nitrite binding, and nitrite binding lowered the reduction potential of the Cu T1 site. The protonation of catalytic His244 subsequent to nitrite binding and T1 Cu reduction induced partial intra-electron transfer from T1 to T2 Cu sites. The proton transfer from His244 to nitrite bound on the T2 Cu site via the hydrogen bond network induced intra-electron transfer from the T1 to T2 Cu site. The interaction of the T1 Cu ligand with the second sphere amino acid residues and water molecules affected the reduction potential of the T1 Cu site. The water molecules in the so-called proton pool have an important role in the regulation of the basicity of His244. The conformation of the sensor loop did not change along the reaction, but the water molecule network extending along the sensor loop was changed by nitrite binding.