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247  structures 4722  species 5  interactions 13598  sequences 86  architectures

Family: RNase_PH (PF01138)

Summary: 3' exoribonuclease family, domain 1

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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 [1]. Q10205 a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.

Literature references

  1. 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:].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan S5 (CL0329), which has the following description:

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

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(192)
Full
(13598)
Representative proteomes NCBI
(10174)
Meta
(6384)
RP15
(1408)
RP35
(2573)
RP55
(3461)
RP75
(4120)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(192)
Full
(13598)
Representative proteomes NCBI
(10174)
Meta
(6384)
RP15
(1408)
RP35
(2573)
RP55
(3461)
RP75
(4120)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(192)
Full
(13598)
Representative proteomes NCBI
(10174)
Meta
(6384)
RP15
(1408)
RP35
(2573)
RP55
(3461)
RP75
(4120)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.1 21.3
Noise cut-off 20.9 20.9
Model length: 132
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

There are 5 interactions for this family. More...

KH_1 PNPase RNase_PH_C RNase_PH S1

Structures

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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