1TF1

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

PDB DOI: 10.2210/pdb1TF1/pdb

Classification: TRANSCRIPTION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-05-26 Released: 2004-08-03
Deposition Author(s): Walker, J.R., Skarina, T., Kudrytska, M., Joachimiak, A., Arrowsmith, C., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.257
R-Value Work: 0.214
R-Value Observed: 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

PubMed: 16546208 Search on PubMed
DOI: 10.1016/j.jmb.2006.02.034
Primary Citation of Related Structures:
1TF1

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.

Related Citations:

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

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 --: --

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative regulator of allantoin and glyoxylate utilization operons	A, B, C, D	198	Escherichia coli	Mutation(s): 0 Gene Names: glxA3
UniProt
Find proteins for P0ACN4 (Escherichia coli (strain K12)) Explore P0ACN4 Go to UniProtKB: P0ACN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ACN4
Protein Feature View Expand
Reference Sequence