5JU7

DNA BINDING DOMAIN OF E.COLI CADC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator.

Schlundt, A.Buchner, S.Janowski, R.Heydenreich, T.Heermann, R.Lassak, J.Geerlof, A.Stehle, R.Niessing, D.Jung, K.Sattler, M.

(2017) Sci Rep 7: 1051-1051

  • DOI: https://doi.org/10.1038/s41598-017-01031-9
  • Primary Citation of Related Structures:  
    5JU7

  • PubMed Abstract: 

    The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC. However, the molecular details for its interaction with DNA have remained elusive. Here, we present the crystal structure of the CadC DNA-binding domain (DBD) and show that it adopts a winged helix-turn-helix fold. The interaction with the cadBA promoter site Cad1 is studied by using nuclear magnetic resonance (NMR) spectroscopy, biophysical methods and functional assays and reveals a preference for AT-rich regions. By mutational analysis we identify amino acids within the CadC DBD that are crucial for DNA-binding and functional activity. Experimentally derived structural models of the CadC-DNA complex indicate that the CadC DBD employs mainly non-sequence-specific over a few specific contacts. Our data provide molecular insights into the CadC-DNA interaction and suggest how CadC dimerization may provide high-affinity binding to the Cad1 promoter.


  • Organizational Affiliation

    Munich Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Technische Universität München, 85748, Garching, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional activator CadC110Escherichia coli K-12Mutation(s): 0 
Gene Names: cadCb4133JW4094
UniProt
Find proteins for P23890 (Escherichia coli (strain K12))
Explore P23890 
Go to UniProtKB:  P23890
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23890
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.14α = 90
b = 104.14β = 90
c = 44γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
REFMACrefinement
Auto-Rickshawphasing
Auto-Rickshawphasing
Auto-Rickshawphasing
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations