Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.76 kDa 
• Atom Count: 1318 
• Residue Count: 155 
• Unique protein chains: 1

3F52

Crystal structure of the clp gene regulator ClgR from C. glutamicum

• DOI: 10.2210/pdb3F52/pdb

• Classification: TRANSCRIPTION ACTIVATOR
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-03 Released: 2008-11-18 
• Deposition Author(s): Russo, S., Schweitzer, J.E., Polen, T., Bott, M., Pohl, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.213 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

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

• PubMed: 19019826 
• DOI: 10.1074/jbc.M806591200
• Primary Citation of Related Structures:  
  3F52, 3F51


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
clp gene regulator (ClgR)	A, E	117	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: cg2152, Cgl1962
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, E	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.213 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.08	α = 90
b = 55.08	β = 90
c = 129.61	γ = 90

Software Package:

Software Name	Purpose
gclient	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-03 
• Released Date: 2008-11-18 
Deposition Author(s): Russo, S., Schweitzer, J.E., Polen, T., Bott, M., Pohl, E.

Revision History 

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance