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 

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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, 1XPR, 1XPU

  • 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 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 ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rho transcription termination factor419Escherichia coliMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P0AG30 (Escherichia coli (strain K12))
Explore P0AG30 
Go to UniProtKB:  P0AG30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG30
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'8N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
BA [auth F],
N [auth A],
P [auth B],
S [auth C],
V [auth D],
BA [auth F],
N [auth A],
P [auth B],
S [auth C],
V [auth D],
Y [auth E]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
BCM
Query on BCM

Download Ideal Coordinates CCD File 
CA [auth F],
Q [auth B],
T [auth C],
W [auth D],
Z [auth E]
BICYCLOMYCIN
C12 H18 N2 O7
WOUDXEYYJPOSNE-VKZDFBPFSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth F],
M [auth A],
O [auth B],
R [auth C],
U [auth D],
AA [auth F],
M [auth A],
O [auth B],
R [auth C],
U [auth D],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BCM BindingDB:  1XPO -TΔS: -2.18e+1 (kJ/mol) from 1 assay(s)
ΔG: -2.51e+1 (kJ/mol) from 1 assay(s)
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

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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