The goal of this project is to obtain an understanding of the function of E. coli DbpA, a member of the large DEAD/H family of proteins that participate in many cellular pathways involving RNA. DEAD/H proteins couple the hydrolysis of ATP with RNA binding and are proposed to modify RNA secondary and tertiary structure. E. Coli DbpA and its B. subtilis homologue YxiN were chosen for detailed structural and mechanistic studies because, unlike nearly all other DEAD/H proteins, they bind tightly and specifically to a discrete region of 23S rRNA. The equilibrium and rate constants for the steps in the minimal kinetic scheme of the ATPase reaction will be determined to establish a framework for structure-function studies. The possibility that DbpA acts as a helicase in restructuring rRNA will be examined. RNA modification, photocrosslinking, and protein engineering experiments will test how different domains of DbpA interact with its cognate RNA, and whether the protein-RNA contacts change during the catalytic cycle. Finally, a DbpA disruption strain of E. coli will be used to search for the mechanism of action of DbpA in E. coli cells.
