Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.77 kDa 
• Atom Count: 1,894 
• Modelled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 2KEJ

Solution structure of a dimer of LAC repressor DNA-binding domain complexed to its natural operator O2

• PDB DOI: 10.2210/pdb2KEJ/pdb
• NDB: 2KEJ

• Classification: Transcription/DNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-30 Released: 2009-05-19 
• Deposition Author(s): Romanuka, J., Folkers, G., Biris, N., Tishchenko, E., Wienk, H., Kaptein, R., Boelens, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes.

Romanuka, J., Folkers, G.E., Biris, N., Tishchenko, E., Wienk, H., Bonvin, A.M., Kaptein, R., Boelens, R.

(2009) J Mol Biol 390: 478-489

• PubMed: 19450607 
• DOI: 10.1016/j.jmb.2009.05.022
• Primary Citation of Related Structures:  
  2KEI, 2KEJ, 2KEK


• PubMed Abstract: 
  

The structures of a dimeric mutant of the Lac repressor DNA-binding domain complexed with the auxiliary operators O2 and O3 have been determined using NMR spectroscopy and compared to the structures of the previously determined Lac-O1 and Lac-nonoperator complexes. Structural analysis of the Lac-O1 and Lac-O2 complexes shows highly similar structures with very similar numbers of specific and nonspecific contacts, in agreement with similar affinities for these two operators. The left monomer of the Lac repressor in the Lac-O3 complex retains most of these specific contacts. However, in the right half-site of the O3 operator, there is a significant loss of protein-DNA contacts, explaining the low affinity of the Lac repressor for the O3 operator. The binding mode in the right half-site resembles that of the nonspecific complex. In contrast to the Lac-nonoperator DNA complex where no hinge helices are formed, the stability of the hinge helices in the weak Lac-O3 complex is the same as in the Lac-O1 and Lac-O2 complexes, as judged from the results of hydrogen/deuterium experiments.

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Organizational Affiliation: 

Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose operon repressor	A, B	62	Escherichia coli K-12	Mutation(s): 1  Gene Names: lacI, b0345, JW0336
UniProt
Find proteins for P03023 (Escherichia coli (strain K12)) Explore P03023  Go to UniProtKB:  P03023

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*AP*AP*TP*GP*TP*GP*AP*GP*CP*GP*AP*GP*TP*AP*AP*CP*AP*AP*CP*CP*G)-3')	C	23	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*TP*TP*GP*TP*TP*AP*CP*TP*CP*GP*CP*TP*CP*AP*CP*AP*TP*TP*TP*C)-3')	D	23	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Romanuka, J., Folkers, G., Biris, N., Tishchenko, E., Wienk, H., Kaptein, R., Boelens, R.

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Data collection, Database references, Derived calculations