1YNJ

Taq RNA polymerase-Sorangicin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.284 

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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: https://doi.org/10.1038/sj.emboj.7600499
  • Primary Citation of Related Structures:  
    1YNJ, 1YNN

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chain
A, B
314Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU8 (Thermus aquaticus)
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Go to UniProtKB:  Q9KWU8
Entity Groups  
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UniProt GroupQ9KWU8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta chain1,119Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU7 (Thermus aquaticus)
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UniProt GroupQ9KWU7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta' chainD,
E [auth J]
1,524Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9KWU6 (Thermus aquaticus)
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UniProt GroupQ9KWU6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase omega chainF [auth K]99Thermus aquaticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9EVV4 (Thermus aquaticus)
Explore Q9EVV4 
Go to UniProtKB:  Q9EVV4
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UniProt GroupQ9EVV4
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.284 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.19α = 90
b = 199.19β = 90
c = 289.306γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-15
    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: 2024-02-14
    Changes: Data collection, Database references, Derived calculations