Crystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA substrate

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

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The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs.

Czudnochowski, N.Ashley, G.W.Santi, D.V.Alian, A.Finer-Moore, J.Stroud, R.M.

(2014) Nucleic Acids Res 42: 2037-2048

  • DOI: https://doi.org/10.1093/nar/gkt1050
  • Primary Citation of Related Structures:  
    4LAB, 4LGT

  • PubMed Abstract: 

    RluB catalyses the modification of U2605 to pseudouridine (Ψ) in a stem-loop at the peptidyl transferase center of Escherichia coli 23S rRNA. The homolog RluF is specific to the adjacent nucleotide in the stem, U2604. The 1.3 Å resolution crystal structure of the complex between the catalytic domain of RluB and the isolated substrate stem-loop, in which the target uridine is substituted by 5-fluorouridine (5-FU), reveals a covalent bond between the isomerized target base and tyrosine 140. The structure is compared with the catalytic domain alone determined at 2.5 Å resolution. The RluB-bound stem-loop has essentially the same secondary structure as in the ribosome, with a bulge at A2602, but with 5-FU2605 flipped into the active site. We showed earlier that RluF induced a frame-shift of the RNA, moving A2602 into the stem and translating its target, U2604, into the active site. A hydrogen-bonding network stabilizes the bulge in the RluB-RNA but is not conserved in RluF and so RluF cannot stabilize the bulge. On the basis of the covalent bond between enzyme and isomerized 5-FU we propose a Michael addition mechanism for pseudouridine formation that is consistent with all experimental data.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, ProLynx, 455 Mission Bay Blvd., Suite 145, San Francisco, CA 94158, USA and Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 320003, Israel.


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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal large subunit pseudouridine synthase BA,
C [auth D]
255Escherichia coli K-12Mutation(s): 0 
Gene Names: rluB
Find proteins for P37765 (Escherichia coli (strain K12))
Explore P37765 
Go to UniProtKB:  P37765
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37765
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
stem-loop of 23S rRNAB [auth E],
D [auth F]
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on OCS
C [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.94α = 90
b = 42.2β = 102.61
c = 169.43γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-12-06
    Changes: Data collection