PDBsum entry: 1b00

Gene regulation

PDB id: 1b00

Contents

Protein chains

122 a.a. *

Waters ×131

* Residue conservation analysis

PDB id:

1b00

Name:

Gene regulation

Title:

Phob receiver domain from escherichia coli

Structure:

Phosphate regulon transcriptional regulatory protein phob. Chain: a, b. Fragment: receiver domain. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: xl1-blue. Cellular_location: cytoplasm. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.88Å R-factor: 0.210 R-free: 0.280

Authors:

M.Sola,F.X.Gomis-Ruth,L.Serrano,A.Gonzalez,M.Coll

Key ref:

M.Solá et al. (1999). Three-dimensional crystal structure of the transcription factor PhoB receiver domain. J Mol Biol, 285, 675-687. PubMed id: 9878437 DOI: 10.1006/jmbi.1998.2326

Date:

15-Nov-98 Release date: 19-Nov-99

Protein chains

P0AFJ5  (PHOB_ECOLI) -  Phosphate regulon transcriptional regulatory protein phoB

Seq: 229 a.a.

Struc: 122 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: two-component signal transduction system (phosphorelay) (2 terms)
• Biochemical function: two-component response regulator activity (1 term)

DOI no: 10.1006/jmbi.1998.2326

J Mol Biol 285:675-687 (1999)

PubMed id: 9878437

Three-dimensional crystal structure of the transcription factor PhoB receiver domain.

M.Solá, F.X.Gomis-Rüth, L.Serrano, A.González, M.Coll.

ABSTRACT

PhoB is the response regulator of the two-component signal transduction system activated under phosphate starvation conditions. This protein is a transcription factor that activates more than 30 genes of the pho regulon and consists of two domains: a DNA binding domain and a dimerization domain, the latter being homologous to the receiver domain described for two-component response regulators. Activation by phosphorylation induces dimerization of the protein and the consequent binding to the DNA direct repeat pho box, where it promotes the binding of RNA polymerase. In the absence of phosphorylation, the activating dimerization process can be mimicked by deletion of the DNA binding domain. The three-dimensional crystal structure of the receiver domain of PhoB from Escherichia coli has been solved by multiple anomalous diffraction using a gold derivative obtained by co-crystallization, and refined using data to 1.9 A resolution. The crystal structure reveals an alpha/beta doubly wound fold, similar to other known receivers, the most conspicuous difference being the displacement of helix alpha4 towards its N terminus. The active site includes the acidic triad Asp53 (the site of phosphorylation), Asp10 and Glu9. Lys105, from loop beta5alpha5, and Glu88, from helix alpha4, interact with Asp53 via an H-bond and a water bridge, respectively. In the asymmetric unit of the crystal there are two molecules linked by a complementary hydrophobic surface, which involves helix alpha1, loop beta5alpha5 and the N terminus of helix alpha5, and is connected to the active site through the fully conserved residue Lys105 from loop beta5alpha5. The possibility that this surface is the functional surface used for the activating dimerization is discussed.

Selected figure(s)

Figure 2.
Figure 2. (a) Ribbon diagram (MOLMOL; [Koradi et al 1996]) showing the structure of the PhoB receiver domain. The two molecules in the asymmetric unit are depicted with the local dyad vertical in this view. Note that the loop α4β4, at the top of the Figure, does not participate in inter-protein contacts although being located in the same face of the interacting surface. (b) Protein-protein interface representation (BOBSCRIPT; [Esnouf 1997]) viewed along the dyad axis. Residues and secondary structure elements at the interface are shown. Lys105 side-chain is also represented in order to show the connection between the active site and the presumed dimerization surface.

Figure 4.
Figure 4. Stereo view of the active site of (a) molecule A and (b) B (drawn with MOLMOL; [Koradi et al 1996]), showing important residues. Hydrogen bonds are depicted with broken lines. Water molecules as blue spheres. Note, in molecule A, the connection of loop β4α4 and helix α4 with the active site, through Lys105 main-chain and water-bridge Glu88-W5-Asp53.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 675-687) copyright 1999.

Figures were selected by the author.