3EQL

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic myxopyronin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Transcription inactivation through local refolding of the RNA polymerase structure.

Belogurov, G.A.Vassylyeva, M.N.Sevostyanova, A.Appleman, J.R.Xiang, A.X.Lira, R.Webber, S.E.Klyuyev, S.Nudler, E.Artsimovitch, I.Vassylyev, D.G.

(2009) Nature 457: 332-335

  • DOI: 10.1038/nature07510

  • PubMed Abstract: 
  • Structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding. Myxopyronin inhibits ba ...

    Structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding. Myxopyronin inhibits bacterial RNA polymerase (RNAP) by an unknown mechanism. Here we report the structure of dMyx--a desmethyl derivative of myxopyronin B--complexed with a Thermus thermophilus RNAP holoenzyme. The antibiotic binds to a pocket deep inside the RNAP clamp head domain, which interacts with the DNA template in the transcription bubble. Notably, binding of dMyx stabilizes refolding of the beta'-subunit switch-2 segment, resulting in a configuration that might indirectly compromise binding to, or directly clash with, the melted template DNA strand. Consistently, footprinting data show that the antibiotic binding does not prevent nucleation of the promoter DNA melting but instead blocks its propagation towards the active site. Myxopyronins are thus, to our knowledge, a first structurally characterized class of antibiotics that target formation of the pre-catalytic transcription initiation complex-the decisive step in gene expression control. Notably, mutations designed in switch-2 mimic the dMyx effects on promoter complexes in the absence of antibiotic. Overall, our results indicate a plausible mechanism of the dMyx action and a stepwise pathway of open complex formation in which core enzyme mediates the final stage of DNA melting near the transcription start site, and that switch-2 might act as a molecular checkpoint for DNA loading in response to regulatory signals or antibiotics. The universally conserved switch-2 may have the same role in all multisubunit RNAPs.


    Organizational Affiliation

    Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B, K, L
315Thermus thermophilusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9Z9H6 (Thermus thermophilus)
Go to UniProtKB:  Q9Z9H6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, M
1119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, N
1524Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, O
99Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor rpoD
F, P
423Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: sigA
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKW1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MXP
Query on MXP

Download SDF File 
Download CCD File 
D, N
Myxopyronin B
methyl [(1E)-5-{3-[(2E,4E)-2,5-dimethylnona-2,4-dienoyl]-4-hydroxy-2-oxo-2H-pyran-6-yl}pent-1-en-1-yl]carbamate
C23 H31 N O6
QBIHIGNYQFSBGW-NOTXRLOZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MXPIC50: 4990 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 235.001α = 90.00
b = 235.001β = 90.00
c = 254.947γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data scaling
CNSrefinement
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance