A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase

Molecules. 2018 Nov 16;23(11):2997. doi: 10.3390/molecules23112997.


Copper-containing nitrite reductases (CuNiRs) play a key role in the global nitrogen cycle by reducing nitrite (NO₂-) to nitric oxide, a reaction that involves one electron and two protons. In typical two-domain CuNiRs, the electron is acquired from an external electron-donating partner. The recently characterised Rastonia picketti (RpNiR) system is a three-domain CuNiR, where the cupredoxin domain is tethered to a heme c domain that can function as the electron donor. The nitrite reduction starts with the binding of NO₂- to the T2Cu centre, but very little is known about how NO₂- binds to native RpNiR. A recent crystallographic study of an RpNiR mutant suggests that NO₂- may bind via nitrogen rather than through the bidentate oxygen mode typically observed in two-domain CuNiRs. In this work we have used combined quantum mechanical/molecular mechanical (QM/MM) methods to model the binding mode of NO₂- with native RpNiR in order to determine whether the N-bound or O-bound orientation is preferred. Our results indicate that binding via nitrogen or oxygen is possible for the oxidised Cu(II) state of the T2Cu centre, but in the reduced Cu(I) state the N-binding mode is energetically preferred.

Keywords: QM/MM methods; RpNiR; nitrite binding; nitrite reductases; three-domain CuNiRs.

MeSH terms

  • Azurin / chemistry
  • Azurin / metabolism
  • Copper / chemistry
  • Copper / metabolism*
  • Electron Transport
  • Heme / chemistry
  • Heme / metabolism*
  • Models, Molecular
  • Molecular Dynamics Simulation*
  • Nitrite Reductases / chemistry*
  • Nitrite Reductases / metabolism*
  • Nitrites / chemistry
  • Nitrites / metabolism*
  • Oxidation-Reduction
  • Protein Binding
  • Protein Conformation
  • Protein Domains
  • Quantum Theory*
  • Ralstonia pickettii / enzymology


  • Nitrites
  • cupredoxin
  • Azurin
  • Heme
  • Copper
  • Nitrite Reductases
  • nitrite reductase, copper-containing