E-Coli Umud Conformational Dynamics in Response to Dna Damage

The SOS mutagenesis pathway in Escherichia coli involves the induction of at least 57 genes in response to DNA damage, including the umuD gene products. UmuD2 is a homodimer of 139-amino acid subunits that interacts with a RecA/ssDNA nucleoprotein filament resulting in cleavage of its N-terminal 24-amino acids to yield UmuD’. Several models have been proposed wherein the N-terminal arms of UmuD2 are in the cis or trans conformations, with elbows up or down. These conformational variants expose multiple binding surfaces that may be used to interact with other proteins. The goal of our research is to determine the conformation and dynamics of UmuD in an effort to understand its regulatory role in response to DNA damage. Electron paramagnetic resonance spectroscopy (EPR) was used to probe the conformational dynamics of wild-type and variant UmuD proteins. EPR experiments suggest that the UmuD N-terminal arms display a large degree of motion and are largely unbound from the globular domain. UmuD interacts with several proteins including the β-clamp. We are using fluorescently labeled β-clamp to determine the conformational change of the β-clamp upon binding to UmuD. Preliminary results suggest that full-length UmuD physically opens the clamp, similar to the action of the δ-subunit of the clamp-loader complex. Research supported by NSF Career MCB-0845033.