Crystal structure of CbnR, a LysR family transcriptional regulator

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

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Crystal Structure of a Full-length LysR-type Transcriptional Regulator, CbnR: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend

Muraoka, S.Okumura, R.Ogawa, N.Nonaka, T.Miyashita, K.Senda, T.

(2003) J Mol Biol 328: 555-566

  • DOI: https://doi.org/10.1016/s0022-2836(03)00312-7
  • Primary Citation of Related Structures:  
    1IXC, 1IZ1

  • PubMed Abstract: 

    The LysR-type transcriptional regulator (LTTR) proteins are one of the most common transcriptional regulators in prokaryotes. Here we report the crystal structure of CbnR, which is one of the LTTRs derived from Ralstonia eutropha NH9. This is the first crystal structure of a full-length LTTR. CbnR was found to form a homo-tetramer, which seems to be a biologically active form. Surprisingly, the tetramer can be regarded as a dimer of dimers, whereby each dimer is composed of two subunits in different conformations. In the CbnR tetramer, the DNA-binding domains are located at the V-shaped bottom of the main body of the tetramer, and seem to be suitable to interact with a long stretch of the promoter DNA, which is approximately 60bp. Interaction between the four DNA-binding domains and the two binding sites on the target DNA is likely to bend the target DNA along the V-shaped bottom of the CbnR tetramer. The relaxation of the bent DNA, which occurs upon inducer binding to CbnR, seems to be associated with a quaternary structure change of the tetramer.

  • Organizational Affiliation

    Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysR-type regulatory protein
A, B
294Cupriavidus necatorMutation(s): 5 
Gene Names: cbnR
Find proteins for Q9WXC7 (Cupriavidus necator)
Explore Q9WXC7 
Go to UniProtKB:  Q9WXC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WXC7
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.22α = 90
b = 100.856β = 90
c = 87.735γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations