 Exoribonuclease

An exoribonuclease is an enzyme that removes nucleotide units successively from an end of an RNA chain. The prefix exo describes end-directed action, in contrast to cleavage at an internal position. The attacked end must be specified: RNase R acts3′→5′, whereas Xrn1 acts5′→3′.^[ref][ref]

End removal has a different inventory from an internal cut. In an idealized 100-nucleotide chain, 20 successive single-nucleotide removal events leave an 80-nucleotide chain. One internal cut can split that same original chain into two fragments while retaining all 100 nucleotides in those fragments. A change in fragment size therefore needs interpretation alongside product amounts and the type of cleavage.

Direction is also distinct from processivity, the persistence of successive reactions during one binding encounter. Binding to an end, removing a nucleotide and remaining associated are separable parts of an enzyme's behavior. End accessibility, RNA structure and terminal chemistry can all affect which substrates are degraded.

The 2011 structural and biochemical study of Xrn1 illustrates why the whole protein matters. Crystal structures of a defined construct were combined with mutational tests; regions remote from the active site helped stabilize its catalytic architecture. Thus a lost degradation signal after deleting a region need not mean that the deleted region itself contains the bond-cleaving chemistry.^[ref]