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TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs . The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft .
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 [PUBMED:10529181]:
Kaya Y, Ofengand J; , RNA 2003;9:711-721.: A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. PUBMED:12756329 EPMC:12756329 .
Ericsson UB, Nordlund P, Hallberg BM; , FEBS Lett 2004;565:59-64.: X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. PUBMED:15135053 EPMC:15135053.