Summary: 3' exoribonuclease family, domain 1
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3' exoribonuclease family, domain 1 Provide feedback
This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, P46948 Q12277 and P25359 contain a copy of this domain . Q10205 a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.
Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D; , Cell 1997;91:457-466.: The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'-->5' exoribonucleases. PUBMED:9390555 EPMC:9390555
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001247
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) [PUBMED:17084501], as well as in archaeal and eukaryotic RNA exosomes [PUBMED:15951817, PUBMED: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 [PUBMED: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 [PUBMED:16713559, PUBMED:17380186].
This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer alpha/beta structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes [PUBMED:9390555].
More information about these proteins can be found at Protein of the Month: RNA Exosomes [PUBMED:].
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This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.
The clan contains the following 14 members:ChlI DNA_mis_repair EFG_IV Fae GHMP_kinases_N IGPD Lon_C LpxC Ribonuclease_P Ribosomal_S5_C RNase_PH Topo-VIb_trans UPF0029 Xol-1_N
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Curation and family details
|Seed source:||Bateman A|
|Author:||Bateman A, Finn RD, Griffiths-Jones SR|
|Number in seed:||192|
|Number in full:||13598|
|Average length of the domain:||132.80 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||40.48 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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There are 5 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RNase_PH domain has been found. There are 247 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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