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 

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

  • 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

    Munich Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Technische Universit√§t M√ľnchen, 85748, Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional activator CadC
A
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: cadC
Find proteins for P23890 (Escherichia coli (strain K12))
Go to UniProtKB:  P23890
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
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 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 104.140α = 90.00
b = 104.140β = 90.00
c = 44.000γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
Auto-Rickshawphasing
Auto-Rickshawphasing
Auto-Rickshawphasing
Auto-Rickshawphasing
Auto-Rickshawphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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