The transcriptional regulator PehR regulates the synthesis
of the
extracellular plant cell wall-degrading enzyme polygalacturonase,
which is essential in the bacterial wilt of plants caused by one of
the most devastating plant phytopathogens, Ralstonia
solanacearum. The bacterium has a wide global distribution
infecting many different plant species, resulting in massive agricultural
and economic losses. Because the PehR molecular structure has not
yet been determined and the structural consequences of PehR on ligand
binding have not been thoroughly investigated, we have used an in silico approach combined with in vitro experiments for the first time to characterize the PehR regulator
from a local isolate (Tezpur, Assam, India) of the phytopathogenic
bacterium R. solanacearum F1C1. In
this study, an in silico approach was employed to
model the 3D structure of the PehR regulator, followed by the binding
analysis of different ligands against this regulatory protein. Molecular
docking studies suggest that ATP has the highest binding affinity
for the PehR regulator. By using molecular dynamics (MD) simulation
analysis, involving root-mean-square deviation, root-mean-square fluctuations,
hydrogen bonding, radius of gyration, solvent-accessible surface area,
and principal component analysis, it was possible to confirm the sudden
conformational changes of the PehR regulator caused by the presence
of ATP. We used an in vitro approach to further validate
the formation of the PehR-ATP complex. In this approach, recombinant
DNA technology was used to clone, express, and purify the gene encoding
the PehR regulator from R. solanacearum F1C1. Purified PehR was used in ATP-binding experiments using fluorescence
spectroscopy and Fourier transform infrared spectroscopy, the outcomes
of which showed a potent binding to ATP. The putative PehR-ATP-binding
analysis revealed the importance of the amino acids Lys190, Glu191, Arg192, Arg375, and Asp378 for the ATP-binding process, but further study is required
to confirm this. It will be simpler to comprehend the catalytic mechanisms
of a crucial PehR regulator process in R. solanacearum with the aid of the ATP-binding process hints provided by these
structural biology applications.