InterPro domain: IPR001656

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 ].

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 [ 4 , 5 ]:

• Pseudouridine synthase I, TruA.
• Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.
• Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.
• Pseudouridine synthase RluA. RluC and RluD belong to this family.
• 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.

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
4. Role of cysteine residues in pseudouridine synthases of different families. Biochemistry 38, 13106-11
5. Enzymatic characterization and mutational studies of TruD--the fifth family of pseudouridine synthases. Arch. Biochem. Biophys. 489, 15-9