Backbone Dynamics of Escherichia coli Ribonuclease HI: Correlations with Structure and Function in an Active Enzyme

Ribonuclease H is an endonuclease that hydrolyzes the RNA moiety of RNA–DNA duplex molecules. Escherichia coliribonuclease H is involved in DNA replication, and retroviral ribonuclease H is essential for reverse transcription of the viral genome. To characterize the intramolcular dynamical properties of E. coliribonuclease H, spin-lattic relaxation rate constants, spin-spin relaxation rate constants and steady state nuclear Overhauser effects for the 15N nuclear spins were measured by using proton-detected heteronuclear NMR spectroscopy. The relaxation data were analyzed by using a series of dynamical models in conjunction with a statistical model selection protocol. Ribonuclease H exhibits a complex array of dynamical features, most notably in the parallel β-strands of the principal five-stranded β-sheet, the coiled-coil helical interface, the active site, and the loop regions surrounding the active site. The dynamical properties are correlated with local structural environments of the 15N spins and suggest possible relationships to the functional properties of ribonuclease H. Results for E. coliribonuclease H are compared to previously reported results for the human immunodeficiancy virus type 1 ribonuclease H domain of reverse transcriptase.