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391  structures 8424  species 0  interactions 31605  sequences 275  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


Internal database links

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 ].

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 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(145)
Full
(31605)
Representative proteomes UniProt
(122299)
RP15
(5103)
RP35
(15620)
RP55
(29948)
RP75
(47467)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(145)
Full
(31605)
Representative proteomes UniProt
(122299)
RP15
(5103)
RP35
(15620)
RP55
(29948)
RP75
(47467)
Alignment:
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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
(145)
Full
(31605)
Representative proteomes UniProt
(122299)
RP15
(5103)
RP35
(15620)
RP55
(29948)
RP75
(47467)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD , Griffiths-Jones SR
Number in seed: 145
Number in full: 31605
Average length of the domain: 133.00 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 40.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.5 25.5
Trusted cut-off 25.5 25.5
Noise cut-off 25.4 25.4
Model length: 132
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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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 391 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096TT32 View 3D Structure Click here
A0A0G2K5A0 View 3D Structure Click here
A0A0R0EVK5 View 3D Structure Click here
A0A0R0EVK5 View 3D Structure Click here
A0A0R0FKW9 View 3D Structure Click here
A0A0R0FKW9 View 3D Structure Click here
A0A0R0FNH9 View 3D Structure Click here
A0A0R0HAK3 View 3D Structure Click here
A0A0R0LKL0 View 3D Structure Click here
A0A0R4ITZ7 View 3D Structure Click here
A0A0R4IV90 View 3D Structure Click here
A0A1D6FJV7 View 3D Structure Click here
A0A1D6GD35 View 3D Structure Click here
A0A1D6GX62 View 3D Structure Click here
A0A1D6HD56 View 3D Structure Click here
A0A1D6HD56 View 3D Structure Click here
A0A1D6HT49 View 3D Structure Click here
A0A1D6HT49 View 3D Structure Click here
A0A1D6I819 View 3D Structure Click here
A0A1D6IKI0 View 3D Structure Click here
A0A1D6KK97 View 3D Structure Click here
A0A1D6LT60 View 3D Structure Click here
A0A1D6NLY0 View 3D Structure Click here
A0A1D6P5A0 View 3D Structure Click here
A0A1D6PYF0 View 3D Structure Click here
A0A1D6PYF2 View 3D Structure Click here
A0A1D8PDW1 View 3D Structure Click here
A0A1D8PHQ0 View 3D Structure Click here
A0A1D8PLY1 View 3D Structure Click here
A0A1D8PS88 View 3D Structure Click here
A0A368UGP1 View 3D Structure Click here
A0A5K1K8M9 View 3D Structure Click here
A2RVK7 View 3D Structure Click here
A4HRM9 View 3D Structure Click here
A4I017 View 3D Structure Click here
A4I8H0 View 3D Structure Click here
A4ID90 View 3D Structure Click here
A4IDR7 View 3D Structure Click here
B4G0W6 View 3D Structure Click here
B7ELW5 View 3D Structure Click here
B9G2C8 View 3D Structure Click here
D3ZW38 View 3D Structure Click here
D4A4Y0 View 3D Structure Click here
F1LSX7 View 3D Structure Click here
G3V6G7 View 3D Structure Click here
G3V6G7 View 3D Structure Click here
G3V6K3 View 3D Structure Click here
G5EDS8 View 3D Structure Click here
G5EG59 View 3D Structure Click here
I1JD36 View 3D Structure Click here
I1KWF8 View 3D Structure Click here
I1L6L3 View 3D Structure Click here
I1LL42 View 3D Structure Click here
I1LR48 View 3D Structure Click here
I1M9D1 View 3D Structure Click here
I1MA04 View 3D Structure Click here
I1MNS7 View 3D Structure Click here
I1MTV9 View 3D Structure Click here
I1N5H9 View 3D Structure Click here
I1N5H9 View 3D Structure Click here
K7KH23 View 3D Structure Click here
K7M466 View 3D Structure Click here
K7MU78 View 3D Structure Click here
K7N096 View 3D Structure Click here
O42872 View 3D Structure Click here
O42894 View 3D Structure Click here
O60124 View 3D Structure Click here
O74918 View 3D Structure Click here
O96177 View 3D Structure Click here
P05055 View 3D Structure Click here
P05055 View 3D Structure Click here
P0CG19 View 3D Structure Click here
P25359 View 3D Structure Click here
P46948 View 3D Structure Click here
P48240 View 3D Structure Click here
P53256 View 3D Structure Click here
P9WGZ7 View 3D Structure Click here
P9WI57 View 3D Structure Click here
P9WI57 View 3D Structure Click here
Q05636 View 3D Structure Click here
Q06265 View 3D Structure Click here
Q10205 View 3D Structure Click here
Q12277 View 3D Structure Click here
Q15024 View 3D Structure Click here
Q17533 View 3D Structure Click here
Q1LVM3 View 3D Structure Click here
Q20128 View 3D Structure Click here
Q29QQ9 View 3D Structure Click here
Q2FZ20 View 3D Structure Click here
Q2FZ20 View 3D Structure Click here
Q2QT85 View 3D Structure Click here
Q4CYY1 View 3D Structure Click here
Q4CZ56 View 3D Structure Click here
Q4D355 View 3D Structure Click here
Q4D6A9 View 3D Structure Click here
Q4D743 View 3D Structure Click here
Q4DGF6 View 3D Structure Click here
Q4DJB2 View 3D Structure Click here
Q4DQ29 View 3D Structure Click here
Q4DWN5 View 3D Structure Click here
Q4DZV2 View 3D Structure Click here
Q4QR75 View 3D Structure Click here
Q4VBT6 View 3D Structure Click here
Q54CU6 View 3D Structure Click here
Q54EU6 View 3D Structure Click here
Q54Q83 View 3D Structure Click here
Q54VM4 View 3D Structure Click here
Q55BB0 View 3D Structure Click here
Q55BJ2 View 3D Structure Click here
Q59X53 View 3D Structure Click here
Q5AMR4 View 3D Structure Click here
Q5RKV6 View 3D Structure Click here
Q5XJQ5 View 3D Structure Click here
Q69LE7 View 3D Structure Click here
Q69LE7 View 3D Structure Click here
Q69T30 View 3D Structure Click here
Q69UI6 View 3D Structure Click here
Q6KAI0 View 3D Structure Click here
Q6KAI0 View 3D Structure Click here
Q6P0I8 View 3D Structure Click here
Q75LC8 View 3D Structure Click here
Q84T68 View 3D Structure Click here
Q8BTW3 View 3D Structure Click here
Q8GZQ3 View 3D Structure Click here
Q8GZQ3 View 3D Structure Click here
Q8ID62 View 3D Structure Click here
Q8ILI7 View 3D Structure Click here
Q8K1R3 View 3D Structure Click here
Q8K1R3 View 3D Structure Click here
Q8T4A9 View 3D Structure Click here
Q8TCS8 View 3D Structure Click here
Q8TCS8 View 3D Structure Click here
Q921I9 View 3D Structure Click here
Q95QG7 View 3D Structure Click here
Q965N3 View 3D Structure Click here
Q965N3 View 3D Structure Click here
Q96B26 View 3D Structure Click here
Q9CRA8 View 3D Structure Click here
Q9D0M0 View 3D Structure Click here
Q9D753 View 3D Structure Click here
Q9FPI0 View 3D Structure Click here
Q9JHI7 View 3D Structure Click here
Q9LDM2 View 3D Structure Click here
Q9LX74 View 3D Structure Click here
Q9M209 View 3D Structure Click here
Q9N4P9 View 3D Structure Click here
Q9NPD3 View 3D Structure Click here
Q9NQT4 View 3D Structure Click here
Q9P7R3 View 3D Structure Click here
Q9S7G6 View 3D Structure Click here
Q9S7G6 View 3D Structure Click here
Q9SP08 View 3D Structure Click here
Q9V9X7 View 3D Structure Click here
Q9V9X7 View 3D Structure Click here
Q9VGZ2 View 3D Structure Click here
Q9VK19 View 3D Structure Click here
Q9VW53 View 3D Structure Click here
Q9ZUI4 View 3D Structure Click here