 Xrn1

Xrn1 is an exoribonuclease that degrades RNA from its $5^{\prime }$ end toward its $3^{\prime }$ end. It hydrolyzes successive phosphodiester bonds, releasing nucleoside monophosphates. Xrn1 participates in cytoplasmic messenger RNA turnover, and terminal chemistry helps determine which substrates it can attack.^[ref]

A short sequence makes the direction concrete. For $5^{\prime }$-ACGU-$3^{\prime }$, initial removal of A leaves CGU. By contrast, polynucleotide phosphorylase acting at the other end first removes U. An internal cut and sequential end removal therefore leave different intermediate patterns even if both eventually destroy the same original molecule.

A substrate-complex study identified a pocket recognizing the terminal $5^{\prime }$ monophosphate. The crystallized complex used a truncated, catalytically impaired protein with a short DNA oligonucleotide; biochemical assays separately tested RNA degradation. That distinction matters when connecting a static structure to the behavior of an active enzyme.^[ref]

The same study tested defined RNA–DNA hybrids with different single-stranded RNA overhangs. Degradation through the paired region occurred with five- and eight-nucleotide $5^{\prime }$ extensions but failed with a two-nucleotide extension under the tested conditions. This supports coupling of hydrolysis to strand separation after productive end engagement, without claiming that every structured RNA is equally accessible.^[ref]

End chemistry, structure and processivity thus describe separate constraints. A terminal monophosphate can favor recognition while an inaccessible end or an obstructing structure still limits degradation.