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427  structures 8634  species 0  interactions 33449  sequences 285  architectures

Family: RNase_PH (PF01138)

Summary: 3' exoribonuclease family, domain 1

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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


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...

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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.

Representative proteomes UniProt
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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.

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Representative proteomes UniProt

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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.

Representative proteomes UniProt
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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...


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: 33449
Average length of the domain: 132.9 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 40.07 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -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: 24
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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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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The tree shows the occurrence of this domain across different species. More...


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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 427 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
A0A044SIN0 View 3D Structure Click here
A0A044SNR0 View 3D Structure Click here
A0A044ULP2 View 3D Structure Click here
A0A044USE3 View 3D Structure Click here
A0A077YX33 View 3D Structure Click here
A0A077YYZ3 View 3D Structure Click here
A0A077YZU3 View 3D Structure Click here
A0A077Z9B3 View 3D Structure Click here
A0A077ZAN7 View 3D Structure Click here
A0A077ZFX6 View 3D Structure Click here
A0A077ZHU7 View 3D Structure Click here
A0A096TT32 View 3D Structure Click here
A0A0D2DEK9 View 3D Structure Click here
A0A0D2DI41 View 3D Structure Click here
A0A0D2FDC1 View 3D Structure Click here
A0A0D2G5Z8 View 3D Structure Click here
A0A0D2GHH2 View 3D Structure Click here
A0A0D2GMU2 View 3D Structure Click here
A0A0G2K5A0 View 3D Structure Click here
A0A0H3GY04 View 3D Structure Click here
A0A0H3H4J2 View 3D Structure Click here
A0A0H5S0J8 View 3D Structure Click here
A0A0H5S6Q3 View 3D Structure Click here
A0A0I9R2U8 View 3D Structure Click here
A0A0J9XYP4 View 3D Structure Click here
A0A0K0E021 View 3D Structure Click here
A0A0K0E144 View 3D Structure Click here
A0A0K0E560 View 3D Structure Click here
A0A0K0E7D9 View 3D Structure Click here
A0A0K0IQL3 View 3D Structure Click here
A0A0K0JMI7 View 3D Structure Click here
A0A0N4U2B7 View 3D Structure Click here
A0A0N4U6M4 View 3D Structure Click here
A0A0N4UC99 View 3D Structure Click here
A0A0N4UG76 View 3D Structure Click here
A0A0N4UHB1 View 3D Structure Click here
A0A0N4ULY5 View 3D Structure Click here
A0A0R0EVK5 View 3D Structure Click here
A0A0R0FKW9 View 3D Structure Click here
A0A0R0FNH9 View 3D Structure Click here