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30  structures 8669  species 0  interactions 20779  sequences 124  architectures

Family: PseudoU_synth_1 (PF01416)

Summary: tRNA pseudouridine synthase

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tRNA pseudouridine synthase Provide feedback

Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis.

Literature references

  1. Arluison V, Hountondji C, Robert B, Grosjean H; , Biochemistry 1998;37:7268-7276.: Transfer RNA-pseudouridine synthetase Pus1 of Saccaromyces cerevisiae contains one atom of zinc essential for its native conformation and tRNA recognition. PUBMED:9585540 EPMC:9585540


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020097

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.

TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [ PUBMED:10625422 , PUBMED:17466622 ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis [ PUBMED:9585540 ]. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique.

This entry represents pseudouridine synthase I (TruA) alpha/beta domain.

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

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...

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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
(262)
Full
(20779)
Representative proteomes UniProt
(85480)
RP15
(3499)
RP35
(10608)
RP55
(20060)
RP75
(32361)
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PP/heatmap 1            

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

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

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  Seed
(262)
Full
(20779)
Representative proteomes UniProt
(85480)
RP15
(3499)
RP35
(10608)
RP55
(20060)
RP75
(32361)
Alignment:
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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
(262)
Full
(20779)
Representative proteomes UniProt
(85480)
RP15
(3499)
RP35
(10608)
RP55
(20060)
RP75
(32361)
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: swissprot
Previous IDs: PseudoU_synt;
Type: Domain
Sequence Ontology: SO:0000417
Author: Howe K , Griffiths-Jones SR
Number in seed: 262
Number in full: 20779
Average length of the domain: 106.90 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 45.56 %

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 23.3 23.3
Trusted cut-off 23.3 23.3
Noise cut-off 23.2 23.2
Model length: 108
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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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 PseudoU_synth_1 domain has been found. There are 30 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
A0A0G2K730 View 3D Structure Click here
A0A0P0VYX7 View 3D Structure Click here
A0A0R0F7R0 View 3D Structure Click here
A0A0R0K9F1 View 3D Structure Click here
A0A1D6HBJ9 View 3D Structure Click here
A0A1D6HFJ4 View 3D Structure Click here
A0A1D6LQ68 View 3D Structure Click here
A0A1D6MYK1 View 3D Structure Click here
A1A6J3 View 3D Structure Click here
A2ADA5 View 3D Structure Click here
A4HYB9 View 3D Structure Click here
A4I5I4 View 3D Structure Click here
A4I9K1 View 3D Structure Click here
B0BN58 View 3D Structure Click here
B4FLR5 View 3D Structure Click here
B7ZX30 View 3D Structure Click here
C0H4R3 View 3D Structure Click here
E1JIR1 View 3D Structure Click here
F1QBS4 View 3D Structure Click here
F1QJL2 View 3D Structure Click here
F1QWW1 View 3D Structure Click here
F4JZU2 View 3D Structure Click here
I1JGM9 View 3D Structure Click here
I1JSA0 View 3D Structure Click here
I1KPQ1 View 3D Structure Click here
I1MJV5 View 3D Structure Click here
K7KAA8 View 3D Structure Click here
K7KAB0 View 3D Structure Click here
K7LKT0 View 3D Structure Click here
K7LVD0 View 3D Structure Click here
K7LZ80 View 3D Structure Click here
K7N408 View 3D Structure Click here
O22928 View 3D Structure Click here
O74451 View 3D Structure Click here
O94295 View 3D Structure Click here
O94396 View 3D Structure Click here
P07649 View 3D Structure Click here
P31115 View 3D Structure Click here
P53167 View 3D Structure Click here
P9WHP9 View 3D Structure Click here