Abstract of the PDB Structure's related Publication:
The pseudouridine (Psi) synthases Pus7p and TruD define a family of RNA-modifying enzymes with no sequence similarity to previously characterized Psi synthases. The 2.2 A resolution structure of Escherichia coli TruD reveals a U-shaped molecule with a catalytic domain that superimposes closely on that of other Psi synthases. A domain that appears to be unique to TruD/Pus7p family enzymes hinges over the catalytic domain, possibly serving to clasp the substrate RNAs. The active site comprises residues that are conserved in other Psi synthases, although at least one comes from a structurally distinct part of the protein. Remarkably, the connectivity of the structural elements of the TruD catalytic domain is a circular permutation of that of its paralogs. Because the sequence of the permuted segment, a beta-strand that bisects the catalytic domain, is conserved among orthologs from bacteria, archaea and eukarya, the permutation likely happened early in evolution.
Five pseudo (Y)-uridine synthases are conserved across all three life domains, including eukarya,
bacteria, and archaea. In E.coli, these are named RluA, RsuA, TruA, TruB, and TruD. These families
share poor sequence similarity. Nonetheless, these families share a core with a common fold and a conserved
This fold consists of an eight-stranded mixed beta-sheet with several helices and loops flanking the catalytic
a cleft that bisects the sheet.
Each of these families carries an essential aspartate residue that is catalytically active. This is the only residue
that is absolutely conserved in all the Y-synthases.
Depending on the enzyme, each core is additionally decorated with several secondary structural elements (
Hamma et al. 2006).
TruD is responsible for synthesis of pseudouridine from uracil-13 in E.coli tRNAs (
Del Campo et al. 2001). The catalytically conserved aspartate
is in position 80 (Asp80) .