Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA pseudouridine(65) synthase
Synonym: YqcB
GI: 108936020
Orf: yqcB, b2791
COG: COG0564
UniProt: P0AA41
Alpha Fold Predicted Structure: AF-P0AA41-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: t:65 - Y



Protein sequence:

MLEILYQDEWLVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIIGDSKHGDLRQNRSGAEHFGLQRLMLHASQLSLTHPFTGEPLTIHAGLDDTWMQALSQFGWRGLLPENERVEFSAPSGQDGEISS

Comments:

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). TruC is responsible for synthesis of pseudouridine from uracil-65 in E.coli tRNAs ( Del Campo et al. 2001). The catalytically conserved aspartate is in position 54 (Asp54) .




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA tRNA 65 GUC GUC tRNAAspGUC TΨC-stem loop Prokaryotic Cytosol 11720289   
U:Y RNA tRNA 65 GAU GAU tRNAIleGAU TΨC-stem loop Prokaryotic Cytosol 11720289   

Alpha Fold Predicted Structure:






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Protein sequence:

M L E I L Y Q D E W L V A V N K P S G W L V H R S W L D R D E K V V V M Q T V R D Q I G Q H V F T A H R L D R P T S G V L L M G L S S E A G R L L A Q Q F E Q H Q I Q K R Y H A I V R G W L M E E A V L D Y P L V E E L D K I A D K F A R E D K G P Q P A V T H Y R G L A T V E M P V A T G R Y P T T R Y G L V E L E P K T G R K H Q L R R H L A H L R H P I I G D S K H G D L R Q N R S G A E H F G L Q R L M L H A S Q L S L T H P F T G E P L T I H A G L D D T W M Q A L S Q F G W R G L L P E N E R V E F S A P S G Q D G E I S S

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-P0AA41-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0AA41-F1.cif  
DSSP Secondary Structures   P0AA41.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. Del Campo M, Kaya Y, Ofengand J RNA [details] 11720289 -