Exoribonuclease, exosome complex <p>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.</p><p>PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [<cite idref="PUB00035567"/>], as well as in archaeal and eukaryotic RNA exosomes [<cite idref="PUB00035568"/>, <cite idref="PUB00035569"/>], 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 [<cite idref="PUB00035570"/>]. 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 [<cite idref="PUB00035571"/>, <cite idref="PUB00035572"/>].</p><p>This entry represents a family of archaeal proteins that are orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in <taxon tax_id="2287">Sulfolobus solfataricus</taxon>, so members of this family are designated exosome complex exonuclease 1, after usage in UniProtKB/Swiss-Prot [<cite idref="PUB00015469"/>].</p>