Crystal Structure of E. coli pseudouridine synthase RluE

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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This is version 1.4 of the entry. See complete history


The Crystal Structure of E. coli rRNA Pseudouridine Synthase RluE.

Pan, H.Ho, J.D.Stroud, R.M.Finer-Moore, J.

(2007) J Mol Biol 367: 1459-1470

  • DOI: https://doi.org/10.1016/j.jmb.2007.01.084
  • Primary Citation of Related Structures:  
    2OLW, 2OML

  • PubMed Abstract: 

    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.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94143, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal large subunit pseudouridine synthase E
A, B
217Escherichia coliMutation(s): 0 
Gene Names: rluE
EC: 5.4.99
Find proteins for P75966 (Escherichia coli (strain K12))
Explore P75966 
Go to UniProtKB:  P75966
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP75966
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DTT

Download Ideal Coordinates CCD File 
C4 H10 O2 S2
Query on SO4

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O4 S
Query on ACY

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth B]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
C2 H4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.015α = 90
b = 78.887β = 90
c = 84.182γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description