Xrn1 (source code)
= Xrn1
{c}
\b[Xrn1] is an <exoribonuclease> that degrades <RNA> from its $5'$ end toward its $3'$ 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.<Structural and biochemical studies of the 5′→3′ exoribonuclease Xrn1 by Jeong Ho Chang and others>[Introduction, cytosolic RNA turnover; Figure5, terminally phosphorylated RNA degradation]{ref}
A short sequence makes the direction concrete. For $5'$-ACGU-$3'$, 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 $5'$ 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.<Coupled 5′ nucleotide recognition and processivity in Xrn1-mediated mRNA decay by Martin Jinek and others>[Results, Structure Determination and Figure3, phosphate recognition and mutational assays]{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 $5'$ 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.<Coupled 5′ nucleotide recognition and processivity in Xrn1-mediated mRNA decay by Martin Jinek and others>[Figure4, matched hybrid substrates with2-,5-,8-nucleotide overhangs]{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.
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