PDBsum entry 2iyn

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protein metals Protein-protein interface(s) links
Transcription PDB id
Protein chains
110 a.a. *
124 a.a. *
_MG ×3
Waters ×108
* Residue conservation analysis
PDB id:
Name: Transcription
Title: The co-factor-induced pre-active conformation in phob
Structure: Phosphate regulon transcriptional regulatory prot chain: a, b, c. Fragment: receiver domain, residues 1-127. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 511693.
2.08Å     R-factor:   0.233     R-free:   0.305
Authors: M.Sola,D.L.Drew,A.G.Blanco,F.X.Gomis-Ruth,M.Coll
Key ref:
M.Solà et al. (2006). The cofactor-induced pre-active conformation in PhoB. Acta Crystallogr D Biol Crystallogr, 62, 1046-1057. PubMed id: 16929106 DOI: 10.1107/S0907444906024541
19-Jul-06     Release date:   30-Aug-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0AFJ5  (PHOB_ECOLI) -  Phosphate regulon transcriptional regulatory protein PhoB
229 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P0AFJ5  (PHOB_ECOLI) -  Phosphate regulon transcriptional regulatory protein PhoB
229 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     two-component signal transduction system (phosphorelay)   1 term 
  Biochemical function     two-component response regulator activity     1 term  


DOI no: 10.1107/S0907444906024541 Acta Crystallogr D Biol Crystallogr 62:1046-1057 (2006)
PubMed id: 16929106  
The cofactor-induced pre-active conformation in PhoB.
M.Solà, D.L.Drew, A.G.Blanco, F.X.Gomis-Rüth, M.Coll.
PhoB is an Escherichia coli transcription factor from a two-component signal transduction system that is sensitive to limiting environmental phosphate conditions. It consists of an N-terminal receiver domain (RD) and a C-terminal DNA-binding domain. The protein is activated upon phosphorylation at the RD, an event that depends on Mg(2+) binding. The structure of PhoB RD in complex with Mg(2+) is presented, which shows three protomers in the asymmetric unit that interact across two different surfaces. One association is symmetric and has been described as a non-active dimerization contact; the other involves the alpha4-beta5-alpha5 interface and recalls the contact found in activated PhoB. However, here this last interaction is not perfectly symmetric and helix alpha4, which in the activated molecule undergoes a helical shift, becomes strongly destabilized in one of the interacting monomers. All protomers bind the cation in a similar manner but, interestingly, at the prospective binding site for the phosphate moiety the side chains of either Glu88 (in helix alpha4) or Trp54 alternate and interact with active-site atoms. When Glu88 is inside the cavity, helix alpha4 is arranged similarly to the unliganded wild-type structure. However, if Trp54 is present, the helix loses its contacts with the active-site cavity and vanishes. Accordingly, the presence of Trp54 in the active site induces a flexible state in helix alpha4, potentially allowing a helical shift that phosphorylation would eventually stabilize.
  Selected figure(s)  
Figure 1.
Figure 1 PhoB RD in complex with Mg^2+. (a) Richardson diagram of the three molecules present in the crystal asymmetric unit: Mg-A (blue), Mg-B (orange) and Mg-C (red). The magnesium ions are represented as green spheres and the coordinating protein residue side chains are shown as ball-and-stick models. (b) Richardson diagram of the PhoB RD molecule Mg-B. Helices are shown as blue ribbons and labelled ( 1- 5) and -strands as orange arrows ( 1- 5). The positions of the N- and the C-termini are also depicted. The green sphere signifies the bound magnesium ion. (c) Superimposition of the C^ traces of the dimers linked through an 1-L 5 5 interface as found in WT-A/B (white), Mg-A/B (orange) and Mg-C/C' (red). Note that helix 3 undergoes a rigid-body displacement on going from the apo protomer (on the right) to one of the magnesium-bound molecules. (d) The 1-L 5 5 interface made up by Mg-A (right, blue) and Mg-B (left, orange). The monomers are superimposed on their Connolly solid surface and have been rotated to show the surfaces in contact. The Mg^2+ ions coordinated in the active site are depicted as green spheres. The residues engaged in homodimeric interactions are shown by their number and their percentage of conservation (see §-2), ranging from 0% (pale yellow) to 100% (red). (e) Mg-A/B dimer superimposed with its Connolly solid surface coloured according to its electrostatic potential, from red (-20k[B]T/e) to blue (+20k[B]T/e). The view is the same as in Fig. 1-(a), as indicated in the thumbnail. Note the continuous electronegative depression connecting both active sites, which contain Mg^2+ ions shown as green spheres. (f) Stereo plot showing the final (2mF[obs] - dF[calc]) electron density (contoured at 1 ) superimposed with the final refined model around the cation-binding site of Mg-C. Intervening residues are displayed as sticks and labelled, as are participating solvent molecules (red spheres) and the magnesium cation (orange sphere). Hydrogen bonds and salt bridges are shown as violet lines and provided with a label indicating the distance (in Å) between the interacting atoms.
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 1046-1057) copyright 2006.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21283542 M.S.Antunes, K.J.Morey, J.J.Smith, K.D.Albrecht, T.A.Bowen, J.K.Zdunek, J.F.Troupe, M.J.Cuneo, C.T.Webb, H.W.Hellinga, and J.I.Medford (2011).
Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway.
  PLoS One, 6, e16292.  
20171928 Y.J.Hsieh, and B.L.Wanner (2010).
Global regulation by the seven-component Pi signaling system.
  Curr Opin Microbiol, 13, 198-203.  
19371748 T.R.Mack, R.Gao, and A.M.Stock (2009).
Probing the roles of the two different dimers mediated by the receiver domain of the response regulator PhoB.
  J Mol Biol, 389, 349-364.  
17182055 R.Arribas-Bosacoma, S.K.Kim, C.Ferrer-Orta, A.G.Blanco, P.J.Pereira, F.X.Gomis-Rüth, B.L.Wanner, M.Coll, and M.Solà (2007).
The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation.
  J Mol Biol, 366, 626-641.
PDB codes: 2jb9 2jba
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