Molecular recognition of mRNA 5′ cap by 3′ poly(A)-specific ribonuclease (PARN) differs from interactions known for other cap-binding proteins

The mRNA 5′ cap structure plays a pivotal role in coordination of eukaryotic translation and mRNA degradation. Poly(A)-specific ribonuclease (PARN) is a dimeric exoribonuclease that efficiently degrades mRNA 3′ poly(A) tails while also simultaneously interacting with the mRNA 5′ cap. The cap binding amplifies the processivity of PARN action. We used surface plasmon resonance kinetic analysis, quantitative equilibrium fluorescence titrations and circular dichroism to study the cap binding properties of PARN. The molecular mechanism of 5′ cap recognition by PARN has been demonstrated to differ from interactions seen for other known cap-binding proteins in that: i) the auxiliary biological function of 5′ cap binding by the 3′ degrading enzyme is accomplished by negative cooperativity of PARN dimer subunits; ii) non-coulombic interactions are major factors in the complex formation; and iii) PARN has versatile activity toward alternative forms of the cap. These characteristics contribute to stabilization of the PARN–cap complex needed for the deadenylation processivity. Our studies provide a consistent biophysical basis for elucidation of the processive mechanism of PARN-mediated 3′ mRNA deadenylation and provide a new framework to interpret the role of the 5′ cap in mRNA degradation. [Display omitted] •5′ mRNA cap recognition by PARN is distinct from other known cap-binding proteins.•Two cap-binding sites of the PARN dimer exhibit a negative cooperativity.•Non-coulombic interactions are major factors in the PARN–cap interaction.•Slow kinetics of assembly and dissociation provides stabilization of the complex.•PARN has versatile activity toward alternative forms of the 5′ cap