Summary: Pseudouridine synthase II TruB, C-terminal
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Pseudouridine synthase II TruB, C-terminal Provide feedback
Members of this family adopt a secondary structure consisting of a four-stranded beta sheet and one alpha helix. They are predominantly RNA-binding domains, mostly found in Pseudouridine synthase II TruB .
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This tab holds annotation information from the InterPro database.
InterPro entry IPR015240
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]. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) [PUBMED:15028724].
|Molecular function||RNA binding (GO:0003723)|
|pseudouridine synthase activity (GO:0009982)|
|Biological process||RNA modification (GO:0009451)|
|pseudouridine synthesis (GO:0001522)|
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This clan consists of the RNA binding PUA domain and ASCH domain. It also contains uncharacterised protein families.
The clan contains the following 10 members:ASCH DUF3850 EVE LON PUA PUA_2 TruB-C_2 TruB_C UPF0113 YTH
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Curation and family details
|Number in seed:||98|
|Number in full:||1516|
|Average length of the domain:||58.00 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||18.73 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
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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-C_2 domain has been found. There are 3 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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