D
IPR011760

Pseudouridine synthase, TruD, insertion domain

InterPro entry
Short namePsdUridine_synth_TruD_insert
Overlapping
homologous
superfamilies
 

Description

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 α+β 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
[2, 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. TruC, 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 α+β subdomain.


Pseudouridine synthase TruD modifies uracil-13 in tRNA
[1]
. TruD belongs to a large family of pseudouridine synthases present in all kingdoms of life
[3]
. It 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 an α/β structure that forms a compact fold titled away from the catalytic domain to create 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
[4]
.

References

1.A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. Kaya Y, Ofengand J. RNA 9, 711-21, (2003). View articlePMID: 12756329

2.Role of cysteine residues in pseudouridine synthases of different families. Ramamurthy V, Swann SL, Spedaliere CJ, Mueller EG. Biochemistry 38, 13106-11, (1999). View articlePMID: 10529181

3.X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. Ericsson UB, Nordlund P, Hallberg BM. FEBS Lett. 565, 59-64, (2004). View articlePMID: 15135053

4.Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold. Hoang C, Ferre-D'Amare AR. RNA 10, 1026-33, (2004). View articlePMID: 15208439

5.Enzymatic characterization and mutational studies of TruD--the fifth family of pseudouridine synthases. Chan CM, Huang RH. Arch. Biochem. Biophys. 489, 15-9, (2009). View articlePMID: 19664587

GO terms

Cross References

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