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48  structures 4803  species 6  interactions 5359  sequences 25  architectures

Family: TruB_N (PF01509)

Summary: TruB family pseudouridylate synthase (N terminal domain)

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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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002501

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]:

  • Pseudouridine synthase I, TruA.
  • Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.
  • Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif.
  • 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.

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].

This entry represents 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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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(171)
Full
(5359)
Representative proteomes NCBI
(4094)
Meta
(1764)
RP15
(520)
RP35
(968)
RP55
(1305)
RP75
(1566)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(171)
Full
(5359)
Representative proteomes NCBI
(4094)
Meta
(1764)
RP15
(520)
RP35
(968)
RP55
(1305)
RP75
(1566)
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
(171)
Full
(5359)
Representative proteomes NCBI
(4094)
Meta
(1764)
RP15
(520)
RP35
(968)
RP55
(1305)
RP75
(1566)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_792 (release 4.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 171
Number in full: 5359
Average length of the domain: 143.70 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 46.08 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.6 25.6
Trusted cut-off 25.8 25.6
Noise cut-off 25.3 25.5
Model length: 149
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 6 interactions for this family. More...

DKCLD TruB_N TruB_C TruB-C_2 PUA Nop10p

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 TruB_N domain has been found. There are 48 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 seqence.

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