1XPO

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.290 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic bicyclomycin

Skordalakes, E.Brogan, A.P.Park, B.S.Kohn, H.Berger, J.M.

(2005) Structure 13: 99-109

  • DOI: 10.1016/j.str.2004.10.013
  • Primary Citation of Related Structures:  
    1XPO, 1XPU, 1XPR

  • PubMed Abstract: 
  • Rho is a hexameric RNA/DNA helicase/translocase that terminates transcription of select genes in bacteria. The naturally occurring antibiotic, bicyclomycin (BCM), acts as a noncompetitive inhibitor of ATP turnover to disrupt this process. We have det ...

    Rho is a hexameric RNA/DNA helicase/translocase that terminates transcription of select genes in bacteria. The naturally occurring antibiotic, bicyclomycin (BCM), acts as a noncompetitive inhibitor of ATP turnover to disrupt this process. We have determined three independent X-ray crystal structures of Rho complexed with BCM and two semisynthetic derivatives, 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB) and 5a-formylbicyclomycin (FB) to 3.15, 3.05, and 3.15 A resolution, respectively. The structures show that BCM and its derivatives are nonnucleotide inhibitors that interact with Rho at a pocket adjacent to the ATP and RNA binding sites in the C-terminal half of the protein. BCM association prevents ATP turnover by an unexpected mechanism, occluding the binding of the nucleophilic water molecule required for ATP hydrolysis. Our data explain why only certain elements of BCM have been amenable to modification and serve as a template for the design of new inhibitors.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rho transcription termination factorABCDEF419Escherichia coliMutation(s): 0 
EC: 3.6.4
Find proteins for P0AG30 (Escherichia coli (strain K12))
Explore P0AG30 
Go to UniProtKB:  P0AG30
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'G, H, J, K, L, M8N/A
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    AGS
    Query on AGS

    Download CCD File 
    A, B, C, D, E, F
    PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
    C10 H16 N5 O12 P3 S
    NLTUCYMLOPLUHL-KQYNXXCUSA-N
     Ligand Interaction
    BCM
    Query on BCM

    Download CCD File 
    B, C, D, E, F
    BICYCLOMYCIN
    C12 H18 N2 O7
    WOUDXEYYJPOSNE-VKZDFBPFSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A, B, C, D, E, F
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    External Ligand Annotations 
    IDBinding Affinity (Sequence Identity %)
    BCMΔG:  25.1200008392334   kJ/mol  BindingDB
    BCM-TΔS:  21.809999465942383   kJ/mol  BindingDB
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.15 Å
    • R-Value Free: 0.306 
    • R-Value Work: 0.285 
    • R-Value Observed: 0.290 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 211.933α = 90
    b = 111.37β = 108.79
    c = 161.033γ = 90
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    SCALAdata scaling
    AMoREphasing
    REFMACrefinement
    CCP4data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2005-02-08
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Advisory, Version format compliance
    • Version 1.3: 2018-01-31
      Changes: Experimental preparation