Crystal Structure of the clp gene regulator ClgR from Corynebacterium glutamicum

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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This is version 1.4 of the entry. See complete history


Crystal structure of the caseinolytic protease gene regulator, a transcriptional activator in actinomycetes

Russo, S.Schweitzer, J.E.Polen, T.Bott, M.Pohl, E.

(2009) J Biol Chem 284: 5208-5216

  • DOI: https://doi.org/10.1074/jbc.M806591200
  • Primary Citation of Related Structures:  
    3F51, 3F52

  • PubMed Abstract: 

    Human pathogens of the genera Corynebacterium and Mycobacterium possess the transcriptional activator ClgR (clp gene regulator) which in Corynebacterium glutamicum has been shown to regulate the expression of the ClpCP protease genes. ClgR specifically binds to pseudo-palindromic operator regions upstream of clpC and clpP1P2. Here, we present the first crystal structure of a ClgR protein from C. glutamicum. The structure was determined from two different crystal forms to resolutions of 1.75 and 2.05 A, respectively. ClgR folds into a five-helix bundle with a helix-turn-helix motif typical for DNA-binding proteins. Upon dimerization the two DNA-recognition helices are arranged opposite to each other at the protein surface in a distance of approximately 30 A, which suggests that they bind into two adjacent major grooves of B-DNA in an anti-parallel manner. A binding pocket is situated at a strategic position in the dimer interface and could possess a regulatory role altering the positions of the DNA-binding helices.

  • Organizational Affiliation

    Swiss Light Source, Paul Scherrer Institut, Villigen PSI CH-5232, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Clp gene regulator (ClgR)
A, B, C, D, E
A, B, C, D, E, F
117Corynebacterium glutamicumMutation(s): 0 
Gene Names: cg2152Cgl1962Clg1962
Find proteins for Q8NP59 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NP59 
Go to UniProtKB:  Q8NP59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NP59
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.44α = 90
b = 84.82β = 95.87
c = 71.43γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2018-05-30
    Changes: Data collection, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations