Abstract of the PDB Structure's related Publication:
Pseudouridine synthases catalyze the isomerization of specific uridines to pseudouridine in a variety of RNAs, yet the basis for recognition of the RNA sites or how they catalyze this reaction is unknown. The crystal structure of pseudouridine synthase I from Escherichia coli, which, for example, modifies positions 38, 39 and/or 40 in tRNA, reveals a dimeric protein that contains two positively charged, RNA-binding clefts along the surface of the protein. Each cleft contains a highly conserved aspartic acid located at its center. 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. The structure suggests that a dimeric enzyme is required for binding transfer RNA and subsequent pseudouridine formation.
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).
TruA is responsible for the pseudouridylation in positions 38, 39, and 40 in many E.coli tRNAs. The catalytically conserved aspartate
is in position 60 (Asp60) (
Hur et al. 2007).