Structural and Dynamics Characterization of the MerR Family Metalloregulator, CueR, in the Repressed and Active States

Metalloregulators have evolved metal coordination sites that “sense” specific metal ion and upon coordination either activate or inhibit DNA binding, thereby controlling the expression of genes that mediate the intracellular metal concentration. Understanding the interactions among metal, DNA, and its sensor is very important for deciphering the microorganism’s degree of survival in the host organism. In this study, we focused on the Cu(I) E.coli metal sensor, CueR. We utilized electron paramagnetic resonance (EPR) spectroscopy and computation to better understand how Cu(I)-DNA binding is harnessed to drive changes in the structure of CueR, consequently inducing the transcription process. We found that CueR undergoes structural changes upon binding DNA and Cu(I), indicating that CueR plays a significant role in initiating the transcription process. CueR is an all-α, tail-to-tail, homodimer where each monomer is composed of an N-terminal domain (helices 1-through-4) that interacts with DNA, and a C-terminal domain (helices 5-6) that mediates the interaction with the other monomer. We show that the active state is formed when the α1 region approaches the α2-α3 region in the DNA binding domain, and the two DNA binding domains of the CueR dimer are getting closer to each other. Moreover, we indicate that CueR exists in solution both in DNA bound and unbound states. We also discovered that mutations in the metal binding site destabilize the protein and imped dimerization. This research provides a detailed structural mechanism underlying the transcription of metalloregulators.