PROSITE documentation PDOC50984

TRUD domain profile

The most abundant modification seen in structured RNAs (transfer, ribosomal, and splicing RNAs) is the isomerization of uridine (U) to pseudouridine (5-ribosyluracil). Pseudouridine is made by a set of enzymes called pseudouridine synthase, which select specific U residues in a polynucleotide chain for isomerization to pseudouridine. Pseudouridine synthases are ubiquitous as putative synthase genes have been found in all genomes so far sequenced. TruD, a pseudouridine synthase in Escherichia coli, is responsible for modifying U 13 in tRNA-Glu to pseudouridine. Homologs of truD have been identified in eubacteria, archaea, and eukarya. Because all of the organisms known to have pseudouridine 13 in their tRNAs also have a truD homolog, it is reasonable to infer that truD homologs in those organisms with tRNA pseudouridine 13 are the responsible synthases [1].

TruD folds into a V-shaped molecule with two distinct modules: a catalytic domain that differs in sequence but is structurally very similar to the catalytic domain of other pseudouridine synthases and a TRUD domain of ~150 amino acids with a α/β fold (see <PDB:1SI7>). The TRUD domain forms a compact fold that is titled away from the catalytic domain to form a deep cleft in truD which is lined with basic residues from each domain. The TRUD domain is always associated with a truD-type catalytic domain and is not found on its own or attached to another type of protein as a separate module. Furthermore, there are no truD-type catalytic domain that lack the TRUD domain insert. The TRUD domain is characterized by two conserved sequence motifs that form a part of the hydrophobic core. The TRUD domain sequence in the truD family is also characterized by large insertions at several specific sites that are seen in many archaeal and eukaryotic homologs. The TRUD domain is likely to be involved in substrate recognition and may represent a RNA binding module [1].

The profile we developed covers the entire TRUD domain.