1YNN

Taq RNA polymerase-rifampicin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.271 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase

Campbell, E.A.Pavlova, O.Zenkin, N.Leon, F.Irschik, H.Jansen, R.Severinov, K.Darst, S.A.

(2005) Embo J. 24: 674-682

  • DOI: 10.1038/sj.emboj.7600499
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampi ...

    A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP beta subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.


    Related Citations: 
    • Structural mechanism for rifampicin inhibition of bacterial RNA polymerase
      Campbell, E.A.,Korzheva, N.,Mustaev, A.,Murakami, K.,Goldfarb, A.,Darst, S.A.
      (2001) Cell 104: 901


    Organizational Affiliation

    The Rockefeller University, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase alpha chain
A, B
314Thermus aquaticusMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q9KWU8 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase beta chain
C
1119Thermus aquaticusMutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q9KWU7 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase beta' chain
D, J
1524Thermus aquaticusMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q9KWU6 (Thermus aquaticus)
Go to UniProtKB:  Q9KWU6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase omega chain
K
99Thermus aquaticusMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q9EVV4 (Thermus aquaticus)
Go to UniProtKB:  Q9EVV4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
C
RIFAMPICIN
C43 H58 N4 O12
JQXXHWHPUNPDRT-WLSIYKJHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.271 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 200.760α = 90.00
b = 200.760β = 90.00
c = 292.938γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance