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: 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Multiple antibiotic resistance protein marAC [auth A]132Escherichia coliMutation(s): 0 
Gene Names: marA
UniProt
Find proteins for P0ACH5 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ACH5
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chainD84Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssez
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    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
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      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: 
      • OLDERADO: 1XS9 Olderado

      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