8EOT

M. tuberculosis RNAP elongation complex with NusG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase.

Vishwakarma, R.K.Qayyum, M.Z.Babitzke, P.Murakami, K.S.

(2023) Proc Natl Acad Sci U S A 120: e2218516120-e2218516120

  • DOI: https://doi.org/10.1073/pnas.2218516120
  • Primary Citation of Related Structures:  
    8EHQ, 8EJ3, 8EOE, 8EOF, 8EOS, 8EOT, 8EXY

  • PubMed Abstract: 

    NusG is a transcription elongation factor that stimulates transcription pausing in Gram+ bacteria including B. subtilis by sequence-specific interaction with a conserved pause-inducing - 11 TTNTTT -6 motif found in the non-template DNA (ntDNA) strand within the transcription bubble. To reveal the structural basis of NusG-dependent pausing, we determined a cryo-EM structure of a paused transcription complex (PTC) containing RNA polymerase (RNAP), NusG, and the TTNTTT motif in the ntDNA strand. The interaction of NusG with the ntDNA strand rearranges the transcription bubble by positioning three consecutive T residues in a cleft between NusG and the β-lobe domain of RNAP. We revealed that the RNAP swivel module rotation (swiveling), which widens (swiveled state) and narrows (non-swiveled state) a cleft between NusG and the β-lobe, is an intrinsic motion of RNAP and is directly linked to trigger loop (TL) folding, an essential conformational change of all cellular RNAPs for the RNA synthesis reaction. We also determined cryo-EM structures of RNAP escaping from the paused transcription state. These structures revealed the NusG-dependent pausing mechanism by which NusG-ntDNA interaction inhibits the transition from swiveled to non-swiveled states, thereby preventing TL folding and RNA synthesis allosterically. This motion is also reduced by the formation of an RNA hairpin within the RNA exit channel. Thus, the pause half-life can be modulated by the strength of the NusG-ntDNA interaction and/or the stability of the RNA hairpin. NusG residues that interact with the TTNTTT motif are widely conserved in bacteria, suggesting that NusG-dependent pausing is widespread.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
347Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoARv3457cMTCY13E12.10c
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 beta'C [auth D]1,316Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoCRv0668MTCI376.07c
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaD [auth E]110Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoZRv1390MTCY21B4.07
EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusGH [auth G]238Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: nusGRv0639MTCY20H10.20
UniProt
Find proteins for P9WIU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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UniProt GroupP9WIU9
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaI [auth C]1,178Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: rpoBRv0667MTCI376.08c
EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (33-MER)E [auth T]40synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (31-MER)F [auth N]40synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')G [auth R]20synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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 StatesGM131860
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098399

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection