Pathways & interactions
tRNA pseudouridine synthase II, TruB, subfamily 2, C-terminal (IPR015225)
Short name: tRNA_psdUridine_synth_fam2_C
Overlapping homologous superfamilies
- PUA-like superfamily (IPR015947)
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 [PMID: 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 [PMID: 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) [PMID: 15028724].
- PF09142 (TruB_C)