F
IPR001406

Pseudouridine synthase I, TruA

InterPro entry
Short namePsdUridine_synth_TruA
Overlapping
homologous
superfamilies
 
family relationships

Description

This entry represents pseudouridine synthase I (TruA) from prokaryotes and tRNA pseudouridine synthase 1 (Pus1) from eukaryotes, which belongs to the TruA family. TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA
[2, 3]
. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis
[1]
. This protein adopts a dimeric assembly and shows two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. Pus1 from Saccharomyces cerevisiae acts at positions 27 and 28 of tRNAs, at positions 34 and 36 of intron-containing precursor tRNA(Ile), at position 35 in the intron-containing tRNA(Tyr) and at position 44 in U2 snRNA
[8, 6, 5]
. This enzyme also catalyses pseudouridylation of mRNAs
[7]
.

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
[4, 9]
:


 * 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.

References

1.Transfer RNA-pseudouridine synthetase Pus1 of Saccharomyces cerevisiae contains one atom of zinc essential for its native conformation and tRNA recognition. Arluison V, Hountondji C, Robert B, Grosjean H. Biochemistry 37, 7268-76, (1998). View articlePMID: 9585540

2.The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Foster PG, Huang L, Santi DV, Stroud RM. Nat. Struct. Biol. 7, 23-7, (2000). View articlePMID: 10625422

3.How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Hur S, Stroud RM. Mol. Cell 26, 189-203, (2007). View articlePMID: 17466622

4.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

5.Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, Leon-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. Cell 159, 148-162, (2014). PMID: 25219674

6.Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA. Arluison V, Buckle M, Grosjean H. J Mol Biol 289, 491-502, (1999). PMID: 10356324

7.mRNA structure determines modification by pseudouridine synthase 1. Carlile TM, Martinez NM, Schaening C, Su A, Bell TA, Zinshteyn B, Gilbert WV. Nat Chem Biol 15, 966-974, (2019). PMID: 31477916

8.The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity. Motorin Y, Keith G, Simon C, Foiret D, Simos G, Hurt E, Grosjean H. RNA 4, 856-69, (1998). View articlePMID: 9671058

9.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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