 Polynucleotide phosphorylase

Polynucleotide phosphorylase is an enzyme that can remove nucleotides from the $3^{\prime }$ end of RNA by phosphorolysis, releasing nucleoside diphosphates. Its reversible reaction is conventionally writtenwhere ${\mathrm{P}}_{\mathrm{i}}$ is inorganic phosphate and $\mathrm{NDP}$ is the released nucleoside diphosphate. The accepted enzyme classification is EC2.7.7.8.^[ref]

For a sequence-accounting example, start with $5^{\prime }$-ACGU-$3^{\prime }$. One terminal cleavage removes the U unit as uridine diphosphate, leaving ACG. Removing the next unit releases the corresponding G-containing diphosphate. The direction is $3^{\prime }$ toward $5^{\prime }$; phosphate participation and the diphosphate product distinguish this chemistry from hydrolytic cleavage releasing a nucleoside monophosphate.

Under conditions favoring the reverse reaction, nucleoside diphosphates can supply units for chain extension. The reversible reaction itself contains no complementary template, so synthetic activity alone does not establish the sequence-copying mechanism of an RNA polymerase.^[ref]

A 2000 X-ray crystallography study revealed a three-subunit assembly with a central channel. The structure contained a phosphate analogue at catalytic sites but no bound RNA. The proposed connection between the channel, RNA handling and processivity was therefore a structural model, rather than a direct movie of a chain moving through the enzyme.^[ref]