Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12913.50 
• Atom Count: 875 
• Residue Count: 110 
• Unique protein chains: 1

5JU7

DNA BINDING DOMAIN OF E.COLI CADC

• DOI: 10.2210/pdb5JU7/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2016-05-10 Released: 2017-04-26 
• Deposition Author(s): Janowski, R., Schlundt, A., Sattler, M., Niessing, D.

---

Experimental Data Snapshot

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

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

• PubMed: 28432336 
• 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 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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transcriptional activator CadC	A	110	Escherichia 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 104.140	α = 90.00
b = 104.140	β = 90.00
c = 44.000	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
REFMAC	refinement
Auto-Rickshaw	phasing
Auto-Rickshaw	phasing
Auto-Rickshaw	phasing
Auto-Rickshaw	phasing
Auto-Rickshaw	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-05-10 
• Released Date: 2017-04-26 
• Deposition Author(s): Janowski, R., Schlundt, A., Sattler, M., Niessing, D.

Revision History 

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