6VW0

Mycobacterium tuberculosis RNAP S456L mutant open promoter complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.

Lilic, M.Chen, J.Boyaci, H.Braffman, N.Hubin, E.A.Herrmann, J.Muller, R.Mooney, R.Landick, R.Darst, S.A.Campbell, E.A.

(2020) Proc Natl Acad Sci U S A 117: 30423-30432

  • DOI: https://doi.org/10.1073/pnas.2013706117
  • Primary Citation of Related Structures:  
    6VVS, 6VVT, 6VVV, 6VVX, 6VVY, 6VVZ, 6VW0

  • PubMed Abstract: 

    Rifampicin (Rif) is a first-line therapeutic used to treat the infectious disease tuberculosis (TB), which is caused by the pathogen Mycobacterium tuberculosis ( Mtb ). The emergence of Rif-resistant (Rif R ) Mtb presents a need for new antibiotics. Rif targets the enzyme RNA polymerase (RNAP). Sorangicin A (Sor) is an unrelated inhibitor that binds in the Rif-binding pocket of RNAP. Sor inhibits a subset of Rif R RNAPs, including the most prevalent clinical Rif R RNAP substitution found in Mtb infected patients (S456>L of the β subunit). Here, we present structural and biochemical data demonstrating that Sor inhibits the wild-type Mtb RNAP by a similar mechanism as Rif: by preventing the translocation of very short RNAs. By contrast, Sor inhibits the Rif R S456L enzyme at an earlier step, preventing the transition of a partially unwound promoter DNA intermediate to the fully opened DNA and blocking the template-strand DNA from reaching the active site in the RNAP catalytic center. By defining template-strand blocking as a mechanism for inhibition, we provide a mechanistic drug target in RNAP. Our finding that Sor inhibits the wild-type and mutant RNAPs through different mechanisms prompts future considerations for designing antibiotics against resistant targets. Also, we show that Sor has a better pharmacokinetic profile than Rif, making it a suitable starting molecule to design drugs to be used for the treatment of TB patients with comorbidities who require multiple medications.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
347Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WGZ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,179Mycobacterium tuberculosisMutation(s): 1 
Gene Names: rpoBSAMEA2682864_01701
EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,326Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WGY7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega110Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoZERS007672_03979ERS007703_04032ERS007720_04749ERS027652_00548ERS027654_02543ERS027656_03959ERS124361_02246
EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA531Mycobacterium tuberculosisMutation(s): 0 
Gene Names: sigAmysArpoDrpoV
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAG [auth J]111Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rbpA
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-binding transcription factor CarDH [auth M]162Mycobacterium tuberculosisMutation(s): 0 
Gene Names: carD
UniProt
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (65-MER)I [auth O]90Mycobacterium tuberculosis
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (65-MER)J [auth P]90Mycobacterium tuberculosis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references