Crystal structure of the E. coli pseudouridine synthase TruB bound to a T stem-loop RNA
Classification:
LYASE/RNA
Technique:
X-Ray Diffraction
Resolution:
1.85
R value free:
0.211
R value observed:
0.184
R value work:
0.184
Abstract of the PDB Structure's related Publication:
Pseudouridine (Psi) synthases catalyze the isomerization of specific uridines in cellular RNAs to pseudouridines and may function as RNA chaperones. TruB is responsible for the Psi residue present in the T loops of virtually all tRNAs. The close homolog Cbf5/dyskerin is the catalytic subunit of box H/ACA snoRNPs. These carry out the pseudouridylation of eukaryotic rRNA and snRNAs. The 1.85 A resolution structure of TruB bound to RNA reveals that this enzyme recognizes the preformed three-dimensional structure of the T loop, primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA. Structural comparisons with TruB demonstrate that all Psi synthases are descended from a common molecular ancestor.
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
active cleft.
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).
TruB is responsible for synthesis of pseudouridine from uracil-55 in E.coli tRNAs (
Del Campo et al. 2001). The catalytically conserved aspartate
is in position 48 (Asp48) .
Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells.
Gutgsell N, Englund N, Niu L, Kaya Y, Lane BG, Ofengand J
An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation.
Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells.
Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli.
Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis.