Structure and function of formate-dependent cytochrome c nitrite reductase, NrfA

Methods Enzymol. 2011;496:399-422. doi: 10.1016/B978-0-12-386489-5.00016-6.

Abstract

Cytochrome c nitrite reductase, NrfA, catalyzes the six-electron reduction of nitrite, NO(2)(-), to ammonium, NH(4)(+), as the final enzymatic step in the dissimilatory metabolic pathway of nitrite ammonification within the biogeochemical nitrogen cycle. NrfA is a 55-65kDa protein that binds five c-type heme groups via thioether bonds to the cysteines of conserved CXXCH heme attachment motifs. Four of these heme groups are considered to be electron transfer centers, with two histidine residues as axial ligands. The remaining heme group features an unusual CXXCK-binding motif, making lysine the proximal axial ligand and leaving the distal position for the substrate binding site located in a secluded binding pocket within the protein. The substrate nitrite is coordinated to the active site heme iron though the free electron pair at the nitrogen atom and is reduced in a consecutive series of electron and proton transfers to the final product, the ammonium ion. While no intermediates of the reaction are released, NrfA is able to reduce various other nitrogen oxides such as nitric oxide (NO), hydroxylamine (H(2)NOH), and nitrous oxide (N(2)O), but notably also sulfite, providing the only known direct link between the nitrogen and sulfur cycles. NrfA invariably forms stable homodimers, but there are at least two distinct electron transfer systems to the enzyme. In many enterobacterial species, NrfA is linked to the menaquinol pool in the cytoplasmic membrane through a soluble electron carrier, NrfB, that in turn interacts with a membrane-integral quinol dehydrogenase, NrfCD. In δ- and ε-proteobacteria, the dimeric NrfA forms a complex with a small quinol dehydrogenase of the NapC/NirT family, NrfH, allowing a more efficient electron transfer.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / enzymology*
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / isolation & purification
  • Bacterial Proteins / metabolism*
  • Catalytic Domain
  • Crystallography, X-Ray
  • Cytochrome c Group / chemistry*
  • Cytochrome c Group / isolation & purification
  • Cytochrome c Group / metabolism*
  • Cytochromes a1 / chemistry*
  • Cytochromes a1 / isolation & purification
  • Cytochromes a1 / metabolism*
  • Cytochromes c1 / chemistry*
  • Cytochromes c1 / isolation & purification
  • Cytochromes c1 / metabolism*
  • Heme / chemistry
  • Nitrate Reductases / chemistry*
  • Nitrate Reductases / isolation & purification
  • Nitrate Reductases / metabolism*
  • Nitrogen Cycle
  • Protein Conformation
  • Structure-Activity Relationship
  • Substrate Specificity
  • Wolinella / enzymology

Substances

  • Bacterial Proteins
  • Cytochrome c Group
  • Heme
  • Cytochromes a1
  • Cytochromes c1
  • cytochrome C-552
  • Nitrate Reductases
  • nitrate reductase (cytochrome)