Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA pseudouridine(13) synthase
Synonym: YgbO
GI: 2501601
Orf: ygbO, b2745
COG: COG0585
UniProt: Q57261
Structures: | 1SB7 | 1SI7 | 1SZW |
Alpha Fold Predicted Structure: AF-Q57261-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: t:13 - Y


PDB Structures:


1SB7

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The pseudouridine (Psi) synthases Pus7p and TruD define a family of RNA-modifying enzymes with no sequence similarity to previously characterized Psi synthases. The 2.2 A resolution structure of Escherichia coli TruD reveals a U-shaped molecule with a catalytic domain that superimposes closely on that of other Psi synthases. A domain that appears to be unique to TruD/Pus7p family enzymes hinges over the catalytic domain, possibly serving to clasp the substrate RNAs. The active site comprises residues that are conserved in other Psi synthases, although at least one comes from a structurally distinct part of the protein. Remarkably, the connectivity of the structural elements of the TruD catalytic domain is a circular permutation of that of its paralogs. Because the sequence of the permuted segment, a beta-strand that bisects the catalytic domain, is conserved among orthologs from bacteria, archaea and eukarya, the permutation likely happened early in evolution.

Download RCSB-PDB Structures:

Pdb Files   1SB7.pdb   1SI7.pdb   1SZW.pdb  
Pdbx/mmCIF Files   1SB7.cif   1SI7.cif   1SZW.cif  


Protein sequence:

MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQRFGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSWFVATTEELAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAMLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVRELINTTGDYAHIAE

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). TruD is responsible for synthesis of pseudouridine from uracil-13 in E.coli tRNAs ( Del Campo et al. 2001). The catalytically conserved aspartate is in position 80 (Asp80) .




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA tRNA 13 SUC SUC tRNAGluSUC D-stem loop Prokaryotic Cytosol 11720289   
U:Y RNA tRNA 13 UUU UUU tRNALysUUU D-stem-loop Prokaryotic Cytosol
U:Y RNA tRNA 13 {UC {UC tRNAGlu{UC D-stem-loop Prokaryotic Cytosol

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-Q57261-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q57261-F1.cif  
DSSP Secondary Structures   Q57261.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. Kaya Y, Ofengand J RNA [details] 12756329 -
Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold. Hoang C, Ferre-D'Amare AR RNA [details] 15208439 -
Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold. Kaya Y, Del Campo M, Ofengand J, Malhotra A J Biol Chem [details] 14999002 -
X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. Ericsson UB, Nordlund P, Hallberg BM FEBS Lett [details] 15135053 -