Atomistic details of the associative phosphodiester cleavage in humanribonuclease H

Abstract

During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by human RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O3′ oxygen to generate the product state. During the reaction mechanism two Mg²⁺ ions support the formation of a stable associated in-line S_N2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol⁻¹ is in excellent agreement with experimental findings (20.5 kcal mol⁻¹). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.