Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA pseudouridine synthase A
Synonym: TTHA1631
GI: 55981600
COG: COG0101
UniProt: Q5SHU9
Structures: | 1VS3 |
Alpha Fold Predicted Structure: AF-Q5SHU9-F1
Enzyme type: pseudouridine synthase predicted
Position of modification - modification: t:38 - Y
t:39 - Y
t:40 - Y

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

The pseudouridine synthase (Psi synthase) TruA catalyzes the conversion of uridine to pseudouridine at positions 38, 39 and/or 40 in the anticodon stem-loop (ASL) of tRNA. We have determined the crystal structure of TruA from Thermus thermophilus HB8 at 2.25 A resolution. TruA and the other (Psi synthases have a completely conserved active site aspartate, which suggests that the members of this enzyme family share a common catalytic mechanism. The T. thermophilus TruA structure reveals the remarkably flexible structural features in the tRNA-binding cleft, which may be responsible for the primary tRNA interaction. In addition, the charged residues occupying the intermediate positions in the cleft may lead the tRNA to the active site for catalysis. Based on the TruB-tRNA complex structure, the T. thermophilus TruA structure reveals that the tRNA probably makes the melting base pairs move into the cleft, and suggests that a conformational change of the substrate tRNA is necessary to facilitate access to the active site aspartate residue, deep within the cleft.

Download RCSB-PDB Structures:

Pdb Files   1VS3.pdb  
Pdbx/mmCIF Files   1VS3.cif  

Protein sequence:



The homologue from E. coli was biochemically characterized.

Alpha Fold Predicted Structure:

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Protein sequence:

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q5SHU9-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q5SHU9-F1.cif  
DSSP Secondary Structures   Q5SHU9.dssp  


Title Authors Journal Details PubMed Id DOI
Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. Dong X, Bessho Y, Shibata R, Nishimoto M, Shirouzu M, Kuramitsu S, Yokoyama S RNA Biol [details] 17114947 -