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
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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
SCOOP: | TruB_N |
External database links
PROSITE: | PDOC00869 PDOC00885 |
SCOP: | 1ksl |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006145
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 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).
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.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | RNA binding (GO:0003723) |
pseudouridine synthase activity (GO:0009982) | |
Biological process | RNA modification (GO:0009451) |
pseudouridine synthesis (GO:0001522) |
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 TruDAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (37000) |
Representative proteomes | UniProt (171705) |
NCBI (232873) |
Meta (6451) |
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RP15 (4915) |
RP35 (17644) |
RP55 (36234) |
RP75 (63447) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (54) |
Full (37000) |
Representative proteomes | UniProt (171705) |
NCBI (232873) |
Meta (6451) |
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RP15 (4915) |
RP35 (17644) |
RP55 (36234) |
RP75 (63447) |
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Raw Stockholm | |||||||||
Gzipped |
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.
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Curation and family details
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Curation
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: | 37000 |
Average length of the domain: | 149.30 aa |
Average identity of full alignment: | 24 % |
Average coverage of the sequence by the domain: | 48.02 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 160 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 31 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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