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50  structures 8764  species 0  interactions 12145  sequences 104  architectures

Family: TruB_N (PF01509)

Summary: TruB family pseudouridylate synthase (N terminal domain)

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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.

TruB family pseudouridylate synthase (N terminal domain) Provide feedback

Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA [2].

Literature references

  1. Nurse K, Wrzesinski J, Bakin A, Lane BG, Ofengand J; , RNA 1995;1:102-112.: Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli. PUBMED:7489483 EPMC:7489483

  2. Lafontaine DLJ, Bousquet-Antonelli C, Henry Y, Caizergues-Ferrer M, Tollervey D; , Genes Dev 1998;12:527-537.: The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. PUBMED:9472021 EPMC:9472021

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002501

TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA [ PUBMED:11779468 ].

Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are [ PUBMED:10529181 , PUBMED:19664587 ]:

  • Pseudouridine synthase I, TruA.
  • Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.
  • Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.
  • Pseudouridine synthase RluA. RluC and RluD belong to this family.
  • Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain.

This entry represents an N-terminal domain found in pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [ PUBMED:9472021 ].

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 PseudoU_synth (CL0649), which has the following description:

This superfamily was built based on the ECOD classification.

The clan contains the following 7 members:

DKCLD DUF2344 PseudoU_synth_1 PseudoU_synth_2 TruB_C_2 TruB_N TruD


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.

Representative proteomes UniProt
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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: Pfam-B_792 (release 4.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 161
Number in full: 12145
Average length of the domain: 141.9 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 41.56 %

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 27.3 27.3
Trusted cut-off 27.4 27.3
Noise cut-off 27.2 27.2
Model length: 149
Family (HMM) version: 21
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 TruB_N domain has been found. There are 50 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
A0A044SZ61 View 3D Structure Click here
A0A044V418 View 3D Structure Click here
A0A077Z1B8 View 3D Structure Click here
A0A077ZFN6 View 3D Structure Click here
A0A0A2V3J7 View 3D Structure Click here
A0A0D2DEM4 View 3D Structure Click here
A0A0D2GYB3 View 3D Structure Click here
A0A0H3GTP1 View 3D Structure Click here
A0A0K0DWB3 View 3D Structure Click here
A0A0K0EQR2 View 3D Structure Click here
A0A0K0JNJ6 View 3D Structure Click here
A0A0N4UPV3 View 3D Structure Click here
A0A0P0WDZ0 View 3D Structure Click here
A0A0P0Y401 View 3D Structure Click here
A0A175WHI7 View 3D Structure Click here
A0A1C1C8X1 View 3D Structure Click here
A0A1C1CPZ3 View 3D Structure Click here
A0A1D6IJ68 View 3D Structure Click here
A0A1D6IKP8 View 3D Structure Click here
A0A1D6J782 View 3D Structure Click here
A0A1D6LHY7 View 3D Structure Click here
A0A1D6MPT4 View 3D Structure Click here
A0A1D8PN62 View 3D Structure Click here
A0A1P6CDC2 View 3D Structure Click here
A0A3P7DHZ4 View 3D Structure Click here
A0A3P7EC79 View 3D Structure Click here
A0A5K4EFY9 View 3D Structure Click here
A0A5K4F0Q6 View 3D Structure Click here
A0JUU8 View 3D Structure Click here
A0LHM2 View 3D Structure Click here
A0Q0Q4 View 3D Structure Click here
A1B5U1 View 3D Structure Click here
A1K7B7 View 3D Structure Click here
A1R520 View 3D Structure Click here
A1S464 View 3D Structure Click here
A1ST47 View 3D Structure Click here
A1UET1 View 3D Structure Click here
A1UU52 View 3D Structure Click here
A1WLI1 View 3D Structure Click here
A1WXU9 View 3D Structure Click here