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 

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:  

  • 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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rho transcription termination factor
A, B, C, D, E, F
419Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rho (nitA, psuA, rnsC, sbaA, tsu)
EC: 3.6.4.-
Find proteins for P0AG30 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG30
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'G,M,H,J,K,L8N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BCM
Query on BCM

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

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BCMΔG: -25.1 kJ/mol (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 211.933α = 90.00
b = 111.370β = 108.79
c = 161.033γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
REFMACrefinement
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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