1R3E: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit

RNA pseudouridine synthase, TruB, catalyzes pseudouridine formation at U55 in tRNA. This posttranscriptional modification is almost universally conserved and occurs in the T arm of most tRNAs. We determined the crystal structure of Escherichia coli TruB apo enzyme, as well as the structure of Thermotoga maritima TruB in complex with RNA. Comparison of the RNA-free and -bound forms of TruB reveals that this enzyme undergoes significant conformational changes on binding to its substrate. These conformational changes include the ordering of the "thumb loop," which binds right into the RNA hairpin loop, and a 10 degree hinge movement of the C-terminal domain. Along with the result of docking experiments performed on apo TruB, we conclude that TruB recognizes its RNA substrate through a combination of rigid docking and induced fit, with TruB first rigidly binding to its target and then maximizing the interaction by induced fit.
PDB ID: 1R3EDownload
MMDB ID: 159230
PDB Deposition Date: 2003/10/1
Updated in MMDB: 2018/02
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Thermotoga maritima
Similar Structures:
Biological Unit for 1R3E: tetrameric; determined by author
Molecular Components in 1R3E
Label Count Molecule
Protein (1 molecule)
tRNA Pseudouridine Synthase B(Gene symbol: TM0856)
Molecule annotation
Nucleotides(2 molecules)
Molecule annotation
Molecule annotation
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Citing MMDB