Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.91 kDa 
• Atom Count: 903 
• Residue Count: 107 
• Unique protein chains: 1

5JU7

DNA BINDING DOMAIN OF E.COLI CADC

• DOI: 10.2210/pdb5JU7/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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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 

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
• 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 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.

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Organizational Affiliation: 

Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transcriptional activator CadC	A	110	Escherichia coli K-12	Mutation(s): 0  Gene Names: cadC, b4133, JW4094
Find proteins for P23890 (Escherichia coli (strain K12)) Explore P23890  Go to UniProtKB:  P23890

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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 
• R-Value Observed: 0.185 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.14	α = 90
b = 104.14	β = 90
c = 44	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
Auto-Rickshaw	phasing
REFMAC	refinement
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
  Changes: Database references