Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal large subunit pseudouridine synthase E
Synonym: YmfC
GI: 3916025
Orf: ymfC, b1135
COG: COG1187
UniProt: P75966
Structures: | 2OML | 2OLW |
Alpha Fold Predicted Structure: AF-P75966-F1
Enzyme type: pseudouridine synthase
Position of modification - modification: l:2457(2457) - Y


PDB Structures:


2OML

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Pseudouridine synthase RluE modifies U2457 in a stem of 23 S RNA in Escherichia coli. This modification is located in the peptidyl transferase center of the ribosome. We determined the crystal structures of the C-terminal, catalytic domain of E. coli RluE at 1.2 A resolution and of full-length RluE at 1.6 A resolution. The crystals of the full-length enzyme contain two molecules in the asymmetric unit and in both molecules the N-terminal domain is disordered. The protein has an active site cleft, conserved in all other pseudouridine synthases, that contains invariant Asp and Tyr residues implicated in catalysis. An electropositive surface patch that covers the active site cleft is just wide enough to accommodate an RNA stem. The RNA substrate stem can be docked to this surface such that the catalytic Asp is adjacent to the target base, and a conserved Arg is positioned to help flip the target base out of the stem into the enzyme active site. A flexible RluE specific loop lies close to the conserved region of the stem in the model, and may contribute to substrate specificity. The stem alone is not a good RluE substrate, suggesting RluE makes additional interactions with other regions in the ribosome.

Download RCSB-PDB Structures:

Pdb Files   2OLW.pdb   2OML.pdb  
Pdbx/mmCIF Files   2OLW.cif   2OML.cif  


Protein sequence:

MRQFIISENTMQKTSFRNHQVKRFSSQRSTRRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD

Comments:

Site-specific RluE makes pseudouridine at position 2457 in a short stem region of helix 89 of Domain V in 23S RNA. The protein has an active site cleft, conserved in all other pseudouridine synthases, that contains invariant Asp and Tyr residues implicated in catalysis. A positively charged surface patch that covers the active site cleft is just wide enough to accommodate an RNA stem. The RNA substrate stem can be docked to this surface such that the catalytic Asp is adjacent to the target base, and a conserved Arg is positioned to help flip the target base out of the stem into the enzyme active site. However the stem alone is not a good RluE substrate, suggesting RluE makes additional interactions with other regions in the ribosome. A flexible RluE loop lies close to the conserved region of the stem in the model and may contribute to substrate specificity. RluE belongs to the same subgroup of RNA pseudouridine synthases as RsuA, RluB and RluF.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Y RNA rRNA 2457 LSU-23S DOMAIN-V Prokaryotic Cytosol 11720289    17320904   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P75966-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P75966-F1.cif  
DSSP Secondary Structures   P75966.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 -
The crystal structure of E. coli rRNA pseudouridine synthase RluE. Pan H, Ho JD, Stroud RM, Finer-Moore J J Mol Biol [details] 17320904 -