PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons

Related Articles
Cas4 Nuclease and Bacterial Immunity
February 2014
Protein-Nucleic Acid Interaction: Inhibition Through Allostery
July 2013
Stabilizing DNA Single Strands
July 2013
AlkB Homologs
August 2012
Methyl maintenance
May 2012
Follow the RNA leader
December 2011
RNA Chaperone NMB1681
July 2011
Seeing HetR
July 2011
Structure from sequence
July 2011
Added benefits
April 2011
Nitrile Reductase QueF
March 2011
Inhibiting factor
February 2011
Tryptophanyl-tRNA Synthetase
February 2011
Regulating nitrogen assimilation
January 2011
Subtle shifts
January 2011
tRNA Isopentenyltransferase MiaA
August 2010
Mre11 Nuclease
May 2010
Seek and destroy 8-oxoguanine
May 2010
Antibiotics and Ribosome Function
March 2010
Pseudouridine Synthase TruA
November 2009
Get3 into the groove
October 2009
Guanine Nucleotide Exchange Factor Vav1 and Rho GTPase Rac1
October 2009
Proofreading RNA
July 2009
Hda and DNA Replication
June 2009
The elusive helicase
April 2009
Poly(A) RNA recognition
January 2009
Scavenger Decapping Enzyme DcpS
November 2008
Bacteriophage Lambda cII Protein
October 2008
RNase T
July 2008
SARS Coronavirus Nonstructural Protein 1
June 2008

Research Themes DNA and RNA

Pseudouridine Synthase TruA

PSI-SGKB [doi:10.3942/psi_sgkb/fm_2009_11]
Featured System - November 2009
Short description: Evolution is a great tinkerer.

Evolution is a great tinkerer. Over the course of millions of years, cells have honed and refined their machinery, selecting many refinements on the basic processes. We can see a perfect example of this by looking at transfer RNA. They are built by ribosomes in the traditional way, using the four standard types of nucleotides. But then a host of enzymes modify the nucleotides to form many different exotic structures. The most common modification is an isomerization: a uracil base is removed, flipped around, and reattached through one of its carbon atoms, changing uridine to pseudouridine.

Flipped Bases

The change from uridine to pseudouridine is subtle and has a subtle structural effect. The new C-C bond connecting the base to the sugar is more flexible than the typical C-N bond found in canonical nucleotides, however, the pseudouridine ironically makes the RNA strand a bit more rigid. The enhanced rigidity is caused by the new placement of the nitrogen atom. In normal bases the nitrogen atom is used to connect to the sugar, but in pseudouridine it is available to hydrogen bond to water. This water then can form hydrogen bonds with the nearby phosphate atoms, rigidifying the backbone and ultimately enhancing the stacking of bases. This is thought to be the major benefit of pseudouridine: it adds a little extra rigidity to regions of the RNA that need to have a defined structure.

Switch to Pseudouridine

Researchers at CSMP have revealed how Escherichia coli cells modify uridine nucleotides in the anticodon stem loop of transfer RNA. TruA is a pseudouridine synthase that specializes in three positions in the tRNA, positions 38, 39, and 40. These positions are in the critical base-paired region adjacent to the anticodon. The enzyme is a dimer of two identical subunits, which embraces both the 38-40 region of the tRNA and regions farther up the molecule. The enzyme acts on 17 different tRNA molecules in the bacteria cell. It appears to prefer tRNA molecules that are flexible, passing up ones that already have rigid anticodon stem loops. In this way, the enzyme helps the cell fine tune its tRNA, making them rigid but not too rigid for optimal function.

Flexible Embrace and a Flipped Out Base

The crystal structures show the structural basis for TruA's affinity for flexible tRNA molecules. Three different crystals of the enzyme in complex with two different forms of the leucine tRNA where obtained. Comparing the different structures, the tRNA shows a large range of motion. In several structures, the loop is bent outwards away from the enzyme. These structures highlight the importance of a key arginine amino acid for finding the base and pulling it into the active site. Several of the structures showed a conformation that is later in the process of acting on the base, with the loop folding deeper into the active site. In one of these structures, shown here from PDB entry 2nr0, a base is flipped out of the normal base pair and inserted into the active site. In this case it is guanine 39, so the structure is an abortive complex, since the enzyme does not make any changes to guanine bases. But it gives an idea of what might happen when the enzyme shifts to place a uridine in the active site. A conserved aspartate is there, ready to extract and flip the base. To take a closer look at this interaction, click in image below for an interactive Jmol view.

The JSmol tab below displays an interactive JSmol.

Hemolysin BL (PDB entry 2nrj)

The B component of hemolysin BL is shown here with a ribbon diagram. The large alpha helical bundle is shown in magenta and the small beta hairpin, which is thought to be the portion that penetrates into the cell membrane, is colored yellow.


  1. Hur, S. and Stroud, R. M. (2007) How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol. Cell 26, 189-203.

  2. Hur, S., Stroud, R. M. and Finer-Moore, J. (2006) Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective. J. Biol. Chem. 281, 38969-38973.

  3. Hamma, T. and Ferre-D'Amare (2006) Pseudouridine synthases. Chem. Biol. 13, 1125-1135.

  4. Charette, M. and Gray, M. W. (2000) Pseudouridine in RNA: what, where, how, and why. IUBMB Life 49, 341-351.

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health