Dynamics of the heme-binding bacterial gas sensing dissimilative nitrate respiration regulator (DNR) and activation barriers for ligand binding and escape [Molecular Biophysics]

July 18th, 2014 by Lobato, L., Bouzhir-Sima, L., Yamashita, T., Wilson, M. T., Vos, M. H., Liebl, U.

DNR ('dissimilative nitrate respiration regulator') is a heme-binding transcription factor that is involved in the regulation of denitrification in Pseudomonas aeruginosa. In the ferrous deoxy state the heme is 6-coordinate; external NO and CO can replace an internal ligand. Using fluorescence anisotropy, we show that high-affinity sequence-specific DNA binding occurs only when the heme is nitrosylated, consistent with the proposed function of DNR as NO sensor and transcriptional activator. This role is moreover supported by the NO 'trapping' properties revealed by ultrafast spectroscopy that are similar to those of other heme-based NO sensor proteins. Dissociated CO in the heme pocket rebinds essentially barrierless, in competition with migration out of the heme pocket. The latter process is thermally activated (Ea ~7 kJ/mol). This result is compared to other heme proteins, including the homologous CO sensor/transcription factor CooA, variants of the 5-coordinate mycobacterial sensor DosT and the electron transfer protein cytochrome c. This comparison indicates that thermal activation of ligand escape from the heme pocket is specific for systems where an external ligand replaces an internal one. The origin of this finding and possible implications are discussed.
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