= Xrn1 5′-phosphate recognition
{c}
\b[Xrn1 5′-phosphate recognition] is the selective interaction between <Xrn1> and the monophosphate at an <RNA> chain's $5'$ end. The enzyme recognizes the terminal nucleotide in context; free inorganic <phosphate> elsewhere in the sample is not the same substrate feature.
In a structural study of a defined Xrn1 construct, a pocket containing Lys93, Gln97, Arg100 and Arg101 contacted the terminal phosphate, while His41 stacked with the terminal base. Mutating phosphate-pocket residues impaired cleavage and <processivity>, linking a structural contact to enzyme function.<Coupled 5′ nucleotide recognition and processivity in Xrn1-mediated mRNA decay by Martin Jinek and others>[Figure3 and Results, phosphate-binding pocket and mutational tests]{ref}
For a matched-substrate example, compare two RNAs with the same sequence but a $5'$ monophosphate on one and a $5'$ hydroxyl on the other. A difference in reaction progress can then test terminal chemistry while sequence is held fixed. Concentration and turnover regime must also be controlled: the study found that ordinary Xrn1 could degrade hydroxylated RNA under its single-turnover conditions, so monophosphate preference should not be rewritten as an absolute prohibition under every assay condition.<Coupled 5′ nucleotide recognition and processivity in Xrn1-mediated mRNA decay by Martin Jinek and others>[Figure3C and accompanying Results, hydroxylated substrates under single-turnover conditions]{ref}
Recognition also matters after an initial cleavage. The newly exposed end must adopt a productive configuration for the next step. Thus a change at a binding pocket can alter repeated action as well as initial substrate selection; a binding signal alone does not establish productive <hydrolysis>.
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