1XS9

A MODEL OF THE TERNARY COMPLEX FORMED BETWEEN MARA, THE ALPHA-CTD OF RNA POLYMERASE AND DNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 

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This is version 1.4 of the entry. See complete history


Literature

Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA.

Dangi, B.Gronenborn, A.M.Rosner, J.L.Martin, R.G.

(2004) Mol Microbiol 54: 45-59

  • DOI: https://doi.org/10.1111/j.1365-2958.2004.04250.x
  • Primary Citation of Related Structures:  
    1XS9

  • PubMed Abstract: 

    The transcriptional activator, MarA, interacts with RNA polymerase (RNAP) to activate promoters of the mar regulon. Here, we identify the interacting surfaces of MarA and of the carboxy-terminal domain of the alpha subunit of RNAP (alpha-CTD) by NMR-based chemical shift mapping. Spectral changes were monitored for a MarA-DNA complex upon titration with alpha-CTD, and for alpha-CTD upon titration with MarA-DNA. The mapping results were confirmed by mutational studies and retention chromatography. A model of the ternary complex shows that alpha-CTD uses a '265-like determinant' to contact MarA at a surface distant from the DNA. This is unlike the interaction of alpha-CTD with the CRP or Fis activators where the '265 determinant' contacts DNA while another surface of the same alpha-CTD molecule contacts the activator. These results reveal a new versatility for alpha-CTD in transcriptional activation.


  • Organizational Affiliation

    Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Multiple antibiotic resistance protein marAC [auth A]132Escherichia coliMutation(s): 0 
Gene Names: marA
UniProt
Find proteins for P0ACH5 (Escherichia coli (strain K12))
Explore P0ACH5 
Go to UniProtKB:  P0ACH5
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACH5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chain84Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssez
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
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UniProt GroupP0A7Z4
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(P*GP*AP*TP*TP*TP*AP*GP*CP*AP*AP*AP*AP*CP*GP*TP*GP*GP*CP*AP*T)-3'A [auth B]20N/A
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(P*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP*AP*AP*TP*C)-3'B [auth C]20N/A
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection