6VVZ

Mycobacterium tuberculosis RNAP S456L mutant transcription initiation intermediate structure with Sorangicin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1073/pnas.2013706117
  • Primary Citation of Related Structures:  
    6VW0, 6VVS, 6VVT, 6VVV, 6VVY, 6VVX, 6VVZ

  • 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 ...

    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; campbee@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha AB347Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta C1179Mycobacterium tuberculosisMutation(s): 1 
Gene Names: rpoBSAMEA2682864_01701
EC: 2.7.7.6
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta' D1326Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega E110Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpoZERS007672_03979ERS007703_04032ERS007720_04749ERS027652_00548ERS027654_02543ERS027656_03959ERS124361_02246
EC: 2.7.7.6
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA F531Mycobacterium tuberculosisMutation(s): 0 
Gene Names: sigAmysArpoDrpoV
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpA J111Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rbpA
Find proteins for P9WHJ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding transcription factor CarD M162Mycobacterium tuberculosisMutation(s): 0 
Gene Names: carD
Find proteins for P9WJG3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (62-MER)P90Mycobacterium tuberculosis
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Entity ID: 9
MoleculeChainsLengthOrganismImage
DNA (65-MER)O90Mycobacterium tuberculosis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRN
Query on SRN

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C
SORANGICIN A
C47 H66 O11
OTABDKFPJQZJRD-QLGZCQHWSA-N
 Ligand Interaction
ZN
Query on ZN

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D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 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