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 1.1 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: 10.1038/s41598-017-01031-9
  • Structures With Same Primary Citation

  • 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 ...

    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

    Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany. sattler@helmholtz-muenchen.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional activator CadCA110Escherichia coli K-12Mutation(s): 0 
Gene Names: cadCb4133JW4094
Find proteins for P23890 (Escherichia coli (strain K12))
Explore P23890 
Go to UniProtKB:  P23890
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references