3BXF

Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with effector fructose-1,6-bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.

Rezacova, P.Kozisek, M.Moy, S.F.Sieglova, I.Joachimiak, A.Machius, M.Otwinowski, Z.

(2008) Mol.Microbiol. 69: 895-910

  • DOI: 10.1111/j.1365-2958.2008.06318.x
  • Primary Citation of Related Structures:  
  • Also Cited By: 4OQQ, 4OQP

  • PubMed Abstract: 
  • Expression of genes in the gapA operon encoding five enzymes for triose phosphate interconversion in Bacillus subtilis is negatively regulated by the Central glycolytic genes Regulator (CggR). CggR belongs to the large SorC/DeoR family of prokaryotic ...

    Expression of genes in the gapA operon encoding five enzymes for triose phosphate interconversion in Bacillus subtilis is negatively regulated by the Central glycolytic genes Regulator (CggR). CggR belongs to the large SorC/DeoR family of prokaryotic transcriptional regulators, characterized by an N-terminal DNA-binding domain and a large C-terminal effector-binding domain. When no glucose is present in growth media, CggR binds to its target DNA sequence and blocks the transcription of genes in the gapA operon. In the presence of glucose, binding of the known effector molecule fructose-1,6-bisphosphate abolishes this interaction. We have identified dihydroxyacetone phosphate, glucose-6-phosphate and fructose-6-phosphate as additional CggR ligands that can bind to the effector-binding site. Crystal structures of C-CggR, the C-terminal effector-binding domain of CggR, both unliganded as well as in complex with the four ligands at resolutions between 1.65 and 1.80 A reveal unique ligand-specific structural changes in the binding site that affect the dimer interface. Binding affinities of these ligands were determined by isothermal titration calorimetry. Chemical cross-linking shows that CggR oligomerization is mediated through its effector-binding domain, and that binding of the different ligands differentially affects the distribution of oligomers. Electrophoretic mobility shift assays (EMSAs) confirmed a destabilizing effect of fructose-1,6-bisphosphate on the CggR/DNA complex, and also showed similar effects for dihydroxyacetone phosphate. Our results suggest that CggR stability and function may be modulated by various effectors in a complex fashion.


    Organizational Affiliation

    Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA. rezacova@uochb.cas.cz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Central glycolytic gene regulator
A, B
255Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: cggR (yvbQ)
Find proteins for O32253 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O32253
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
13P
Query on 13P

Download SDF File 
Download CCD File 
B
1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
 Ligand Interaction
FBP
Query on FBP

Download SDF File 
Download CCD File 
A
BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
13PKd: 3340 nM BINDINGMOAD
FBPKd: 2870 nM BINDINGMOAD
FBPKd: 2870 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.447α = 90.00
b = 83.245β = 90.00
c = 116.457γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
MOLREPphasing
HKL-3000data scaling
REFMACrefinement
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance