4WJY

Esherichia coli nitrite reductase NrfA H264N

Summary for 4WJY

• Entry DOI: 10.2210/pdb4wjy/pdb
• Related: 2RDZ 2RF7
• Descriptor: Cytochrome c-552, HEME C, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: nitrite reductase cytochrome mutagenesis, oxidoreductase
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 2
• Total formula weight: 107819.69

Authors

Clarke, T.A.,Edwards, M.J.,Lockwood, C.W.J. (deposition date: 2014-10-01, release date: 2015-03-11, Last modification date: 2024-01-10)

Primary citation

Lockwood, C.W.,Burlat, B.,Cheesman, M.R.,Kern, M.,Simon, J.,Clarke, T.A.,Richardson, D.J.,Butt, J.N.
Resolution of key roles for the distal pocket histidine in cytochrome C nitrite reductases.
J.Am.Chem.Soc., 137:3059-3068, 2015

PubMed Abstract: Cytochrome c nitrite reductases perform a key step in the biogeochemical N-cycle by catalyzing the six-electron reduction of nitrite to ammonium. These multiheme cytochromes contain a number of His/His ligated c-hemes for electron transfer and a structurally differentiated heme that provides the catalytic center. The catalytic heme has proximal ligation from lysine, or histidine, and an exchangeable distal ligand bound within a pocket that includes a conserved histidine. Here we describe properties of a penta-heme cytochrome c nitrite reductase in which the distal His has been substituted by Asn. The variant is unable to catalyze nitrite reduction despite retaining the ability to reduce a proposed intermediate in that process, namely, hydroxylamine. A combination of electrochemical, structural and spectroscopic studies reveals that the variant enzyme simultaneously binds nitrite and electrons at the catalytic heme. As a consequence the distal His is proposed to play a key role in orienting the nitrite for N-O bond cleavage. The electrochemical experiments also reveal that the distal His facilitates rapid nitrite binding to the catalytic heme of the native enzyme. Finally it is noted that the thermodynamic descriptions of nitrite- and electron-binding to the active site of the variant enzyme are modulated by the prevailing oxidation states of the His/His ligated hemes. This behavior is likely to be displayed by other multicentered redox enzymes such that there are wide implications for considering the determinants of catalytic activity in this important and varied group of oxidoreductases.

PubMed: 25658043
DOI: 10.1021/ja512941j

Experimental method

X-RAY DIFFRACTION (2.15 Å)