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39  structures 715  species 0  interactions 1161  sequences 27  architectures

Family: tRNA_int_endo_N (PF02778)

Summary: tRNA intron endonuclease, N-terminal domain

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

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.

tRNA intron endonuclease, N-terminal domain Provide feedback

Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9.

Literature references

  1. Kleman-Leyer K, Armbruster DW, Daniels CJ; , Cell 1997;89:839-847.: Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. PUBMED:9200602 EPMC:9200602

  2. Li H, Trotta CR, Abelson J; , Science 1998;280:279-284.: Crystal structure and evolution of a transfer RNA splicing enzyme. PUBMED:9535656 EPMC:9535656


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006678

This entry represents a 2-layer alpha/beta domain found at the N terminus of the homotetrameric tRNA-intron endonucleases [ PUBMED:9535656 ], and as domains 1 (N-terminal) and 3 in the homodimeric enzymes [ PUBMED:16690865 ]. tRNA-intron endonucleases ( EC ) remove tRNA introns by cleaving pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-hydroxyl termini [ PUBMED:9200602 ]. These enzymes recognise a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp [ PUBMED:14993668 ]. Although homotetrameric enzymes contain four active sites, only two participate in the cleavage, and should therefore, be considered as a dimer of dimers.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 tRNA-IECD_N (CL0476), which has the following description:

This superfamily contains families of the N-termini of tRNA-splicing endonucleases.

The clan contains the following 2 members:

tRNA_int_end_N2 tRNA_int_endo_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
(43)
Full
(1161)
Representative proteomes UniProt
(4680)
RP15
(177)
RP35
(506)
RP55
(1011)
RP75
(1549)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(43)
Full
(1161)
Representative proteomes UniProt
(4680)
RP15
(177)
RP35
(506)
RP55
(1011)
RP75
(1549)
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
(43)
Full
(1161)
Representative proteomes UniProt
(4680)
RP15
(177)
RP35
(506)
RP55
(1011)
RP75
(1549)
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: Enright A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Enright A , Ouzounis C , Bateman A , Griffiths-Jones SR
Number in seed: 43
Number in full: 1161
Average length of the domain: 67.9 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 22.34 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 67
Family (HMM) version: 17
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

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 tRNA_int_endo_N domain has been found. There are 39 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
A0A044UGW7 View 3D Structure Click here
A0A0A2VKP8 View 3D Structure Click here
A0A0K0EQT0 View 3D Structure Click here
A0A0N4U0N3 View 3D Structure Click here
A0A5S6P7L7 View 3D Structure Click here
A2BIW2 View 3D Structure Click here
C6T7C2 View 3D Structure Click here
F1QLQ4 View 3D Structure Click here
I1JXC8 View 3D Structure Click here
O07118 View 3D Structure Click here
O07165 View 3D Structure Click here
O29362 View 3D Structure Click here
Q12X51 View 3D Structure Click here
Q2R1K2 View 3D Structure Click here
Q2V3Q6 View 3D Structure Click here
Q3IU70 View 3D Structure Click here
Q4JAF4 View 3D Structure Click here
Q54RX5 View 3D Structure Click here
Q58819 View 3D Structure Click here
Q5JHP5 View 3D Structure Click here
Q5M954 View 3D Structure Click here
Q5UYF6 View 3D Structure Click here
Q5Z6B1 View 3D Structure Click here
Q5ZIN2 View 3D Structure Click here
Q6LY59 View 3D Structure Click here
Q6P7W5 View 3D Structure Click here
Q74MP4 View 3D Structure Click here
Q8IP11 View 3D Structure Click here
Q8NCE0 View 3D Structure Click here
Q8PZI1 View 3D Structure Click here
Q8TGX1 View 3D Structure Click here
Q8TGZ5 View 3D Structure Click here
Q8TGZ7 View 3D Structure Click here
Q8U429 View 3D Structure Click here
Q8ZVI1 View 3D Structure Click here
Q975R3 View 3D Structure Click here
Q97ZY3 View 3D Structure Click here
Q9HN82 View 3D Structure Click here
Q9LSS3 View 3D Structure Click here
Q9M1E8 View 3D Structure Click here