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34  structures 8518  species 0  interactions 42627  sequences 229  architectures

Family: PseudoU_synth_2 (PF00849)

Summary: RNA pseudouridylate synthase

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RNA pseudouridylate synthase 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 RluD P33643 a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA [1].

Literature references

  1. Wrzesinski J, Nurse K, Bakin A, Lane BG, Ofengand J; , RNA 1995;1:437-448.: A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe). PUBMED:7493321 EPMC:7493321


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006145

This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit) and TruC [ PUBMED:11720289 ].

RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [ PUBMED:11953756 , PUBMED:16511038 ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site.

RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine:

  • RluB modifies uracil-2605.
  • RluC modifies uracil-955, U-2504, and U-2580.
  • RluD modifies uracil-1911, U-1915, and U-1917.
  • RluE modifies uracil-3457.
  • RluF modifies uracil-2604, and to a lesser extent U-2605.

RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [ PUBMED:15078091 , PUBMED:14659742 ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different.

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.

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
(54)
Full
(42627)
Representative proteomes UniProt
(202442)
RP15
(6235)
RP35
(20963)
RP55
(42543)
RP75
(72884)
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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.

Format an alignment

  Seed
(54)
Full
(42627)
Representative proteomes UniProt
(202442)
RP15
(6235)
RP35
(20963)
RP55
(42543)
RP75
(72884)
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
(54)
Full
(42627)
Representative proteomes UniProt
(202442)
RP15
(6235)
RP35
(20963)
RP55
(42543)
RP75
(72884)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Pfam-B_421 (release 3.0)
Previous IDs: YABO;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 54
Number in full: 42627
Average length of the domain: 149.80 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 46.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.7
Model length: 160
Family (HMM) version: 24
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_2 domain has been found. There are 34 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
A0A0R0ED85 View 3D Structure Click here
A0A0R0JAL4 View 3D Structure Click here
A0A0R0LPC8 View 3D Structure Click here
A0A1D6F3N1 View 3D Structure Click here
A0A1D6H948 View 3D Structure Click here
A0A1D6HZX2 View 3D Structure Click here
A0A1D6JNZ0 View 3D Structure Click here
A0A1D6JZ25 View 3D Structure Click here
A0A1D6JZ25 View 3D Structure Click here
A0A1D6LMW4 View 3D Structure Click here
A0A1D6MXB5 View 3D Structure Click here
A0A1D8PE33 View 3D Structure Click here
A0A1D8PND6 View 3D Structure Click here
A3BN26 View 3D Structure Click here
A4HRE9 View 3D Structure Click here
A4HS20 View 3D Structure Click here
A4HWD8 View 3D Structure Click here
A4HWD8 View 3D Structure Click here
A4I245 View 3D Structure Click here
A4I5I1 View 3D Structure Click here
A4I5M1 View 3D Structure Click here
A4IC64 View 3D Structure Click here
A4IDD7 View 3D Structure Click here
B1WC14 View 3D Structure Click here
D4A6T2 View 3D Structure Click here
D4ACD4 View 3D Structure Click here
E7FFJ5 View 3D Structure Click here
I1JSZ4 View 3D Structure Click here
I1KC01 View 3D Structure Click here
I1LCX1 View 3D Structure Click here
I1M124 View 3D Structure Click here
I1MFF8 View 3D Structure Click here
I1NHE4 View 3D Structure Click here
K7MNI8 View 3D Structure Click here
K7N2M0 View 3D Structure Click here
K7U1X9 View 3D Structure Click here
O07166 View 3D Structure Click here
O16686 View 3D Structure Click here
O96270 View 3D Structure Click here
P0AA37 View 3D Structure Click here
P0AA39 View 3D Structure Click here
P0AA41 View 3D Structure Click here
P0AA43 View 3D Structure Click here
P32684 View 3D Structure Click here
P33643 View 3D Structure Click here
P37765 View 3D Structure Click here
P53294 View 3D Structure Click here
P75966 View 3D Structure Click here
P9WHQ1 View 3D Structure Click here
P9WHQ3 View 3D Structure Click here
Q06244 View 3D Structure Click here
Q08C69 View 3D Structure Click here
Q09709 View 3D Structure Click here
Q0DST9 View 3D Structure Click here
Q0E0Y3 View 3D Structure Click here
Q0J4D4 View 3D Structure Click here
Q10RN1 View 3D Structure Click here
Q12069 View 3D Structure Click here
Q12362 View 3D Structure Click here
Q149F1 View 3D Structure Click here
Q14AI6 View 3D Structure Click here
Q2FX95 View 3D Structure Click here
Q2FXH7 View 3D Structure Click here
Q2FY78 View 3D Structure Click here
Q2FZ78 View 3D Structure Click here
Q2FZQ6 View 3D Structure Click here
Q2QNM3 View 3D Structure Click here
Q3ECD0 View 3D Structure Click here
Q4CL85 View 3D Structure Click here
Q4CQR7 View 3D Structure Click here
Q4CQR7 View 3D Structure Click here
Q4CS47 View 3D Structure Click here
Q4D881 View 3D Structure Click here
Q4D881 View 3D Structure Click here
Q4D992 View 3D Structure Click here
Q4DB45 View 3D Structure Click here
Q4DGU2 View 3D Structure Click here
Q4DJ27 View 3D Structure Click here
Q4DM27 View 3D Structure Click here
Q4DVT9 View 3D Structure Click here
Q4DXD9 View 3D Structure Click here
Q4QQT0 View 3D Structure Click here
Q54N28 View 3D Structure Click here
Q54N28 View 3D Structure Click here
Q54RS0 View 3D Structure Click here
Q54UF9 View 3D Structure Click here
Q54VB9 View 3D Structure Click here
Q55AQ0 View 3D Structure Click here
Q5A0Y2 View 3D Structure Click here
Q5M721 View 3D Structure Click here
Q5XET6 View 3D Structure Click here
Q5Z8P2 View 3D Structure Click here
Q69K07 View 3D Structure Click here
Q6DBR0 View 3D Structure Click here
Q6P087 View 3D Structure Click here
Q7XA65 View 3D Structure Click here
Q86K31 View 3D Structure Click here
Q8I312 View 3D Structure Click here
Q8I3P7 View 3D Structure Click here
Q8I5D9 View 3D Structure Click here
Q8IZ73 View 3D Structure Click here
Q8L960 View 3D Structure Click here
Q8T866 View 3D Structure Click here
Q8VCZ8 View 3D Structure Click here
Q96CM3 View 3D Structure Click here
Q9CWX4 View 3D Structure Click here
Q9LT72 View 3D Structure Click here
Q9LU60 View 3D Structure Click here
Q9SVS0 View 3D Structure Click here
Q9UJJ7 View 3D Structure Click here
Q9VKU8 View 3D Structure Click here
Q9VKV0 View 3D Structure Click here