Summary: tRNA Pseudouridine synthase II, C terminal
tRNA Pseudouridine synthase II, C terminal Provide feedback
The C terminal domain of tRNA Pseudouridine synthase II adopts a PUA (PF01472) fold, with a four-stranded mixed beta-sheet flanked by one alpha-helix on each side. It allows for binding of the enzyme to RNA, as well as stabilisation of the RNA molecule .
Chaudhuri BN, Chan S, Perry LJ, Yeates TO; , J Biol Chem. 2004;279:24585-24591.: Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft. PUBMED:15028724 EPMC:15028724
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015225
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].
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)|
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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_substr_bdg PUA PUA_2 TruB-C_2 TruB_C UPF0113 YTH
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Number in seed:||26|
|Number in full:||2295|
|Average length of the domain:||56.40 aa|
|Average identity of full alignment:||67 %|
|Average coverage of the sequence by the domain:||18.81 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 domain has been found. There are 2 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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