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7  structures 1702  species 1  interaction 2142  sequences 12  architectures

Family: TruD (PF01142)

Summary: tRNA pseudouridine synthase D (TruD)

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tRNA pseudouridine synthase D (TruD) Provide feedback

TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs [1]. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft [2].

Literature references

  1. Kaya Y, Ofengand J; , RNA 2003;9:711-721.: A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. PUBMED:12756329 EPMC:12756329

  2. Ericsson UB, Nordlund P, Hallberg BM; , FEBS Lett 2004;565:59-64.: X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. PUBMED:15135053 EPMC:15135053


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001656

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.

Pseudouridine synthase TruD modifies uracil-13 in tRNA [PUBMED:12756329]. TruD belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life [PUBMED:15135053]. TruD folds into a V-shaped molecule with an RNA-binding cleft formed between its two domains: a catalytic domain and an insertion domain. The catalytic domain differs in sequence but is structurally very similar to the catalytic domain of other pseudouridine synthases. The insertion (or TRUD) domain displays a novel alpha/beta structure that forms a compact fold titled away from the catalytic domain to form a deep cleft in TruD which is lined with basic residues from each domain. The insertion domain is characterised by two conserved sequence motifs that form a part of the hydrophobic core, as well as by large insertions at several specific sites that are seen in many archaeal and eukaryotic homologues. The insertion domain is likely to be involved in substrate recognition and may represent a RNA binding module [PUBMED:15208439].

Gene Ontology

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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

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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.

  Seed
(69)
Full
(2142)
Representative proteomes NCBI
(1714)
Meta
(284)
RP15
(257)
RP35
(430)
RP55
(625)
RP75
(755)
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Format an alignment

  Seed
(69)
Full
(2142)
Representative proteomes NCBI
(1714)
Meta
(284)
RP15
(257)
RP35
(430)
RP55
(625)
RP75
(755)
Alignment:
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Sequence:
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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.

  Seed
(69)
Full
(2142)
Representative proteomes NCBI
(1714)
Meta
(284)
RP15
(257)
RP35
(430)
RP55
(625)
RP75
(755)
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.

Pfam alignments:

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: Prosite
Previous IDs: none
Type: Family
Author: Finn RD, Bateman A, Moxon SJ
Number in seed: 69
Number in full: 2142
Average length of the domain: 327.60 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 79.21 %

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 19.2 19.2
Trusted cut-off 19.8 19.2
Noise cut-off 19.0 19.0
Model length: 378
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

TruD

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 TruD domain has been found. There are 7 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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