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173  structures 8688  species 0  interactions 37364  sequences 453  architectures

Family: RNase_T (PF00929)

Summary: Exonuclease

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Ribonuclease T". More...

Ribonuclease T Edit Wikipedia article

Ribonuclease T (RNase T, exonuclease T, exo T) is an ribonuclease enzyme involved in the maturation of transfer RNA and ribosomal RNA in bacteria,[1] as well as in DNA repair pathways.[2] It is a member of the DnaQ family of exonucleases and non-processively acts on the 3' end of single-stranded nucleic acids. RNase T is capable of cleaving both DNA and RNA, with extreme sequence specificity discriminating against cytosine at the 3' end of the substrate.[1][3]

References

  1. ^ a b . doi:10.1074/jbc.M204252200. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  2. ^ . doi:10.1371/journal.pbio.1001803. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)
  3. ^ . doi:10.1093/nar/gks548. {{cite journal}}: Cite journal requires |journal= (help); Missing or empty |title= (help)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Exonuclease Provide feedback

This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;

Literature references

  1. Koonin EV, Deutscher MP; , Nucleic Acids Res 1993;21:2521-2522.: RNase T shares conserved sequence motifs with DNA proofreading exonucleases. PUBMED:8506149 EPMC:8506149


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013520

This entry includes a variety of exonuclease proteins, such as ribonuclease T [ PUBMED:8506149 ] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.

Domain organisation

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

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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
(40)
Full
(37364)
Representative proteomes UniProt
(147805)
RP15
(5532)
RP35
(17069)
RP55
(35562)
RP75
(60183)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(40)
Full
(37364)
Representative proteomes UniProt
(147805)
RP15
(5532)
RP35
(17069)
RP55
(35562)
RP75
(60183)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(40)
Full
(37364)
Representative proteomes UniProt
(147805)
RP15
(5532)
RP35
(17069)
RP55
(35562)
RP75
(60183)
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: Pfam-B_1153 (release 3.0)
Previous IDs: Exonuclease; Exonuc_X-T;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 40
Number in full: 37364
Average length of the domain: 160 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 36.48 %

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 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 165
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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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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The tree shows the occurrence of this domain across different species. 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_T domain has been found. There are 173 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
A0A044QTE8 View 3D Structure Click here
A0A044R952 View 3D Structure Click here
A0A044T3D7 View 3D Structure Click here
A0A044TUT5 View 3D Structure Click here
A0A044UDL1 View 3D Structure Click here
A0A077YUT4 View 3D Structure Click here
A0A077Z519 View 3D Structure Click here
A0A077Z6E3 View 3D Structure Click here
A0A077Z6M3 View 3D Structure Click here
A0A077ZBY0 View 3D Structure Click here
A0A077ZCV1 View 3D Structure Click here
A0A077ZKL6 View 3D Structure Click here
A0A077ZL14 View 3D Structure Click here
A0A0A2VLV4 View 3D Structure Click here
A0A0D2D9D4 View 3D Structure Click here
A0A0D2DW34 View 3D Structure Click here
A0A0D2F0T9 View 3D Structure Click here
A0A0D2GSH4 View 3D Structure Click here
A0A0G2KA38 View 3D Structure Click here
A0A0H3GIQ4 View 3D Structure Click here
A0A0H3GP72 View 3D Structure Click here
A0A0H3GQ46 View 3D Structure Click here
A0A0H3GQI6 View 3D Structure Click here
A0A0H3GSG0 View 3D Structure Click here
A0A0H3GWY3 View 3D Structure Click here
A0A0H3H118 View 3D Structure Click here
A0A0H3H6C6 View 3D Structure Click here
A0A0K0DVL5 View 3D Structure Click here
A0A0K0DWV9 View 3D Structure Click here
A0A0K0DXF4 View 3D Structure Click here
A0A0K0DY12 View 3D Structure Click here
A0A0K0DZ28 View 3D Structure Click here
A0A0K0E6Z4 View 3D Structure Click here
A0A0K0J4B4 View 3D Structure Click here
A0A0N4U2F6 View 3D Structure Click here
A0A0N4U2P0 View 3D Structure Click here
A0A0N4U380 View 3D Structure Click here
A0A0N4UAQ7 View 3D Structure Click here
A0A0N4UKQ1 View 3D Structure Click here
A0A0N4URT8 View 3D Structure Click here