Polyribonucleotide nucleotidyltransferase (IPR012162)

Short name: PNPase

Overlapping homologous superfamilies


Family relationships


The eukaryotic exosome and the prokaryotic degradosome are important protein complexes involved in RNA processing and maintaining appropriate RNA levels within the cell [PMID: 11796219]. Both of these complexes contain exoribonucleases (exoRNases) which degrade RNA from the 3' end. The hydrolytic exoRNases produce nucleoside monophosphates, while the phosphorolytic exoRNases add orthophosphate at the cleaved bond to produce nucleoside monophosphates.

This entry represents polyribonucleotide nucleotidyltransferase (EC:, also known as polynucleotide phosphorylase (PNPase), found in bacterial and eukaryotic organelle degradosomes. This enzyme can process single-stranded RNA, but is stalled by double-stranded structures such as stem-loops. Structural studies show that PNPase is a trimeric multidomain protein with a central channel [PMID: 11080643]. Each subunit contains duplicated RNase PH-like domains which, though structurally homologous, are thought to be functionally distinct. The first domain is more divergent in sequence than than the second domain and is thought to be involved in the flexible binding of RNA substrate and the formation of the trimer channel structure. The second domain is thought to contain the catalytic site and show exoRNase activity. The catalytic mechanism of the enzyme is not yet known but it seems likely that single-stranded RNA would be threaded through the channel to be processed by the three active sites within the trimer, which would thus be restricted to a single substrate molecule per trimer. PNPase activity would thus be tightly regulated by secondary structural elements within the RNA [PMID: 17084501].

GO terms

Biological Process

GO:0006402 mRNA catabolic process

Molecular Function

GO:0003723 RNA binding
GO:0004654 polyribonucleotide nucleotidyltransferase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.