1TF1

Crystal Structure of the E. coli Glyoxylate Regulatory Protein Ligand Binding Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR.

Walker, J.R.Altamentova, S.Ezersky, A.Lorca, G.Skarina, T.Kudritska, M.Ball, L.J.Bochkarev, A.Savchenko, A.

(2006) J.Mol.Biol. 358: 810-828

  • DOI: 10.1016/j.jmb.2006.02.034

  • PubMed Abstract: 
  • The interaction of Escherichia coli AllR regulator with operator DNA is disrupted by the effector molecule glyoxylate. This is a general, yet uncharacterized regulatory mechanism for the large IclR family of transcriptional regulators to which AllR b ...

    The interaction of Escherichia coli AllR regulator with operator DNA is disrupted by the effector molecule glyoxylate. This is a general, yet uncharacterized regulatory mechanism for the large IclR family of transcriptional regulators to which AllR belongs. The crystal structures of the C-terminal effector-binding domain of AllR regulator and its complex with glyoxylate were determined at 1.7 and 1.8 A, respectively. Residues involved in glyoxylate binding were explored in vitro and in vivo. Altering the residues Cys217, Ser234 and Ser236 resulted in glyoxylate-independent repression by AllR. Sequence analysis revealed low conservation of amino acid residues participating in effector binding among IclR regulators, which reflects potential chemical diversity of effector molecules, recognized by members of this family. Comparing the AllR structure to that of Thermotoga maritima TM0065, the other representative of the IclR family that has been structurally characterized, indicates that both proteins assume similar quaternary structures as a dimer of dimers. Mutations in the tetramerization region, which in AllR involve the Cys135-Cys142 region, resulted in dissociation of AllR tetramer to dimers in vitro and were functionally inactive in vivo. Glyoxylate does not appear to function through the inhibition of tetramerization. Using sedimentation velocity, glyoxylate was shown to conformationally change the AllR tetramer as well as monomer and dimer resulting in altered outline of AllR molecules.


    Related Citations: 
    • Structural Analyses of the Ligand Binding Sites of the IclR family of transcriptional regulators
      Walker, J.R.,Evdokimova, L.,Zhang, R.G.,Bochkarev, A.,Joachimiak, A.,Arrowsmith, C.,Edwards, A.,Savchenko, A.
      () TO BE PUBLISHED --: --
    • Crystal Structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family
      Zhang, R.G.,Kim, Y.,Skarina, T.,Beasley, S.,Laskowski, R.,Arrowsmith, C.,Edwards, A.,Joachimiak, A.,Savchenko, A.
      (2002) J.Biol.Chem. 277: 19183


    Organizational Affiliation

    Ontario Center for Structural Proteomics, Best Institute, 112 College St., Toronto, Ontario, M5G1L6 Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Negative regulator of allantoin and glyoxylate utilization operons
A, B, C, D
198Escherichia coli (strain K12)Gene Names: allR (glxA3, ybbU)
Find proteins for P0ACN4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACN4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 92.796α = 90.00
b = 97.538β = 90.00
c = 144.488γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation