Exoribonuclease, PH domain 2 superfamily (IPR036345)
Short name: ExoRNase_PH_dom2_sf
- Ribonuclease PH, bacterial-type (IPR002381)
- Exosome complex component Rrp41 (IPR011807)
- Polyribonucleotide nucleotidyltransferase (IPR012162)
- Guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase (IPR014069)
- Exoribonuclease, phosphorolytic domain 2 (IPR015847)
- Exosome complex component Rrp42, archaea (IPR020869)
- PNPase/RNase PH domain superfamily (IPR027408)
- Exosome complex component RRP45 (IPR033100)
- Exosome complex component Rrp43 (IPR033196)
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 the phosphorolytic (PH) domain 2 superfamily. This domain has a core 3-layer alpha/beta/alpha structure. It is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes [PMID: 9390555].
- SSF55666 (SSF55666)