Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.76 kDa 
• Atom Count: 1,711 
• Modelled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 2H3C

Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA

• PDB DOI:  https://doi.org/10.2210/pdb2H3C/pdb
• NDB: 2H3C

• Classification: IMMUNE SYSTEM/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-22 Released: 2006-11-21 
• Deposition Author(s): Madl, T., Van Melderen, L., Respondek, M., Oberer, M., Keller, W., Zangger, K.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural Basis for Nucleic Acid and Toxin Recognition of the Bacterial Antitoxin CcdA

Madl, T., Van Melderen, L., Mine, N., Respondek, M., Oberer, M., Keller, W., Khatai, L., Zangger, K.

(2006) J Mol Biol 364: 170-185

• PubMed: 17007877 
• DOI: https://doi.org/10.1016/j.jmb.2006.08.082
• Primary Citation of Related Structures:  
  2ADL, 2ADN, 2H3A, 2H3C


• PubMed Abstract: 
  

Toxin-antitoxin systems are highly abundant in plasmids and bacterial chromosomes. They ensure plasmid maintenance by killing bacteria that have lost the plasmid. Their expression is autoregulated at the level of transcription. Here, we present the solution structure of CcdA, the antitoxin of the ccd system, as a free protein (16.7 kDa) and in complex with its cognate DNA (25.3 kDa). CcdA is composed of two distinct and independent domains: the N-terminal domain, responsible for DNA binding, which establishes a new family of the ribbon-helix-helix fold and the C-terminal region, which is responsible for the interaction with the toxin CcdB. The C-terminal domain is intrinsically unstructured and forms a tight complex with the toxin. We show that CcdA specifically recognizes a 6 bp palindromic DNA sequence within the operator-promoter (OP) region of the ccd operon and binds to DNA by insertion of the positively charged N-terminal beta-sheet into the major groove. The binding of up to three CcdA dimers to a 33mer DNA of its operator-promoter region was studied by NMR spectroscopy, isothermal titration calorimetry and single point mutation. The highly flexible C-terminal region of free CcdA explains its susceptibility to proteolysis by the Lon ATP-dependent protease.

---

Organizational Affiliation: 

Institute of Chemistry, University of Graz, Graz 8010, Austria.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CcdA	C [auth A], D [auth B]	72	Escherichia coli	Mutation(s): 1
UniProt
Find proteins for P62552 (Escherichia coli (strain K12)) Explore P62552  Go to UniProtKB:  P62552

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'	A [auth C]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3'	B [auth D]	13	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  2H3C	Kd: 8.85e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Madl, T., Van Melderen, L., Respondek, M., Oberer, M., Keller, W., Zangger, K.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Data collection, Database references, Derived calculations