InterPro : IPR012162

Name  Polyribonucleotide nucleotidyltransferase Short Name  PNPase
Type  Family Description  The eukaryotic exosome and the prokaryotic degradosome are important protein complexes involved in RNA processing and maintaining appropriate RNA levels within the cell []. 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 (), 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 []. 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 [].

Sequence Features

GO Displayer


InterPro protein domain ID --> Contigs



1 Child Features

Id Name Short Name Type
IPR014069 Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase pppGpp_PNP Family

8 Contains

Id Name Short Name Type
IPR012340 Nucleic acid-binding, OB-fold NA-bd_OB-fold Domain
IPR004088 K Homology domain, type 1 KH_dom_type_1 Domain
IPR003029 Ribosomal protein S1, RNA-binding domain Rbsml_prot_S1_RNA-bd_dom Domain
IPR020568 Ribosomal protein S5 domain 2-type fold Ribosomal_S5_D2-typ_fold Domain
IPR001247 Exoribonuclease, phosphorolytic domain 1 ExoRNase_PH_dom1 Domain
IPR015847 Exoribonuclease, phosphorolytic domain 2 ExoRNase_PH_dom2 Domain
IPR004087 K Homology domain KH_dom Domain
IPR015848 Polyribonucleotide nucleotidyltransferase, RNA-binding domain PNPase_PH_RNA-bd_bac/org-type Domain

0 Found In

0 Parent Features

3 Publications

First Author Title Year Journal Volume Pages
Briani F Genetic analysis of polynucleotide phosphorylase structure and functions. 2007 Biochimie 89 145-57
Symmons MF A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation. 2000 Structure 8 1215-26
Symmons MF Running rings around RNA: a superfamily of phosphate-dependent RNases. 2002 Trends Biochem Sci 27 11-8

To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)