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

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

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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: https://doi.org/10.1016/j.jmb.2006.02.034
  • Primary Citation of Related Structures:  

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Negative regulator of allantoin and glyoxylate utilization operons
A, B, C, D
198Escherichia coliMutation(s): 0 
Gene Names: glxa3
Find proteins for P0ACN4 (Escherichia coli (strain K12))
Explore P0ACN4 
Go to UniProtKB:  P0ACN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACN4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.796α = 90
b = 97.538β = 90
c = 144.488γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Refinement description