Polyribonucleotide nucleotidyltransferase, RNA-binding domain (IPR015848)

Short name: PNPase_PH_RNA-bd_bac/org-type

Overlapping homologous superfamilies

Domain relationships



The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate.

PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [PMID: 17084501], as well as in archaeal and eukaryotic RNA exosomes [PMID: 15951817, PMID: 17174896], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber [PMID: 16285927]. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [PMID: 16713559, PMID: 17380186].

This entry represents an RNA-binding domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (IPR001247) and PH domain 2 (IPR015847), both of which are found in PNPases and exosomes. The core structure of the RNA-binding domain consists of a DNA/RNA-binding 3-helical bundle.

GO terms

Biological Process

GO:0006396 RNA processing

Molecular Function

GO:0003723 RNA binding

Cellular Component

No terms assigned in this category.

Contributing signatures

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