InterPro domain: IPR042214

Pseudouridine synthase TruD modifies uracil-13 in tRNA [ 1 ]. TruD belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life [ 2 ]. TruD folds into a V-shaped molecule with an RNA-binding cleft formed between its two domains: a catalytic domain and an insertion domain. The catalytic domain differs in sequence but is structurally very similar to the catalytic domain of other pseudouridine synthases. The insertion (or TRUD) domain displays a novel alpha/beta structure that forms a compact fold titled away from the catalytic domain to form a deep cleft in TruD which is lined with basic residues from each domain. The insertion domain is characterised by two conserved sequence motifs that form a part of the hydrophobic core, as well as by large insertions at several specific sites that are seen in many archaeal and eukaryotic homologues. The insertion domain is likely to be involved in substrate recognition and may represent a RNA binding module [ 3 ].

This superfamily represents the catalytic domain of TruD.

1. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 9, 711-21
2. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Lett. 565, 59-64
3. Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold. RNA 10, 1026-33