DNA damage response protein UmuD displays conformational dynamics

Abstract

DNA damage is universal and all organisms have systems in place to respond to such damage. The Escherichia coli umuD gene products are essential to SOS‐induced mutagenesis in response to DNA damage. UmuD is a dynamic 139‐amino acid homodimeric protein that binds to a RecA/ssDNA nucleoprotein filament, which stimulates the latent ability of UmuD to cleave its N‐terminal 24‐amino acids to form UmuD’. The umuD gene products have been shown to perform distinct functions in both preventing and facilitating mutagenesis. Several models have been proposed for the conformation of the UmuD protein including two versions with the arms in trans conformation and two models with the arms in cis conformation. Each conformation exposes different binding surfaces through which UmuD could interact with other proteins. Through the use of models and structural data, it was concluded that structural rearrangement of UmuD occurs upon binding to the RecA filament and upon cleavage. The goal of our research is to determine the conformation and dynamics of the umuD gene products in order to understand how their protein‐protein interactions regulate cellular responses to DNA damage. Electron paramagnetic resonance spectroscopy (EPR) has been employed to probe the conformations of UmuD and UmuD’. Our EPR experiments suggest that the UmuD N‐terminal arms exhibit a large degree of motion. Research supported by NSF Career MCB‐0845033.