Binding Determinants of HIV-1 REV RNA to the Pokeweed Antiviral Protein

The pokeweed antiviral protein (PAP) is an N-glycosidase that removes an adenine residue from the sarcin/ricin loop (SRL) of rRNA through a process called depurination. PAP has also been shown to depurinate the ORF of Rev RNA of HIV-1 in vivo without causing toxicity. The sequence and structure of Rev RNA that PAP interacts is identified and compared to the sarcin/ricin loop in order to describe the importance of RNA structure for PAP specificity. My results show that PAP binds to a short GGGAA sequence at the site of depurination of Rev RNA. Structural analysis reveals that the binding site is within a 15 nt hairpin pentaloop. The pentaloop contains a pseudo GNRA loop structure that swings G and A residues out of the hairpin, allowing PAP access to these purines for binding and depurination. These data provide new insight into the specificity of PAP to target an RNA.