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PDBsum entry 1zes

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protein ligands metals Protein-protein interface(s) links
Transcription activator PDB id
1zes
Jmol
Contents
Protein chains
121 a.a. *
Ligands
BEF ×3
Metals
_MG ×3
Waters ×179
* Residue conservation analysis
PDB id:
1zes
Name: Transcription activator
Title: Bef3- activated phob receiver domain
Structure: Phosphate regulon transcriptional regulatory protein phob. Chain: a, b, c. Fragment: n-terminal domain (residues 1-125). Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: phob. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Other_details: restriction sites nde1, bamh1
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.194     R-free:   0.240
Authors: P.Bachhawat,G.T.Montelione,A.M.Stock
Key ref:
P.Bachhawat et al. (2005). Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states. Structure, 13, 1353-1363. PubMed id: 16154092 DOI: 10.1016/j.str.2005.06.006
Date:
19-Apr-05     Release date:   20-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AFJ5  (PHOB_ECOLI) -  Phosphate regulon transcriptional regulatory protein PhoB
Seq:
Struc:
229 a.a.
121 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: 10.1016/j.str.2005.06.006 Structure 13:1353-1363 (2005)
PubMed id: 16154092  
 
 
Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states.
P.Bachhawat, G.V.Swapna, G.T.Montelione, A.M.Stock.
 
  ABSTRACT  
 
Response regulators (RRs), which undergo phosphorylation/dephosphorylation at aspartate residues, are highly prevalent in bacterial signal transduction. RRs typically contain an N-terminal receiver domain that regulates the activities of a C-terminal DNA binding domain in a phosphorylation-dependent manner. We present crystallography and solution NMR data for the receiver domain of Escherichia coli PhoB which show distinct 2-fold symmetric dimers in the inactive and active states. These structures, together with the previously determined structure of the C-terminal domain of PhoB bound to DNA, define the conformation of the active transcription factor and provide a model for the mechanism of activation in the OmpR/PhoB subfamily, the largest group of RRs. In the active state, the receiver domains dimerize with 2-fold rotational symmetry using their alpha4-beta5-alpha5 faces, while the effector domains bind to DNA direct repeats with tandem symmetry, implying a loss of intramolecular interactions.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal Structures Show Different Dimers for Inactive and Active Regulatory Domains of PhoB
(A) Inactive PhoB[N] dimerizes using the a1-a5 interface. Inactive PhoB[N] is red; the dimer interface is beige.
(B) Active PhoB[N] dimerizes using the a4-b5-a5 interface. Active PhoB[N] is green; the dimer interface is blue; and active site ligands are shown as spheres with magnesium in cyan, beryllium in pink, and fluorides in magenta. Figures were created using Pymol (http://pymol.sourceforge.net/).
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1353-1363) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20702407 C.M.Barbieri, T.R.Mack, V.L.Robinson, M.T.Miller, and A.M.Stock (2010).
Regulation of response regulator autophosphorylation through interdomain contacts.
  J Biol Chem, 285, 32325-32335.
PDB codes: 3nhz 3nnn 3nns
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
20171928 Y.J.Hsieh, and B.L.Wanner (2010).
Global regulation by the seven-component Pi signaling system.
  Curr Opin Microbiol, 13, 198-203.  
19217394 A.R.Kinjo, and H.Nakamura (2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
  Structure, 17, 234-246.  
19199332 K.Wollschläger, K.Gaus, A.Körnig, R.Eckel, S.D.Wilking, M.McIntosh, Z.Majer, A.Becker, R.Ros, D.Anselmetti, and N.Sewald (2009).
Single-molecule experiments to elucidate the minimal requirement for DNA recognition by transcription factor epitopes.
  Small, 5, 484-495.  
19455134 M.S.Antunes, K.J.Morey, N.Tewari-Singh, T.A.Bowen, J.J.Smith, C.T.Webb, H.W.Hellinga, and J.I.Medford (2009).
Engineering key components in a synthetic eukaryotic signal transduction pathway.
  Mol Syst Biol, 5, 270.  
19575571 R.Gao, and A.M.Stock (2009).
Biological insights from structures of two-component proteins.
  Annu Rev Microbiol, 63, 133-154.  
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.  
19432796 U.M.Pinto, and S.C.Winans (2009).
Dimerization of the quorum-sensing transcription factor TraR enhances resistance to cytoplasmic proteolysis.
  Mol Microbiol, 73, 32-42.  
19542275 W.Spencer, R.Siam, M.C.Ouimet, D.P.Bastedo, and G.T.Marczynski (2009).
CtrA, a global response regulator, uses a distinct second category of weak DNA binding sites for cell cycle transcription control in Caulobacter crescentus.
  J Bacteriol, 191, 5458-5470.  
19646451 Y.Pazy, A.C.Wollish, S.A.Thomas, P.J.Miller, E.J.Collins, R.B.Bourret, and R.E.Silversmith (2009).
Matching biochemical reaction kinetics to the timescales of life: structural determinants that influence the autodephosphorylation rate of response regulator proteins.
  J Mol Biol, 392, 1205-1220.
PDB codes: 3f7n 3fft 3ffw 3ffx 3fgz
18832306 D.Ruiz, P.Salinas, M.L.Lopez-Redondo, M.L.Cayuela, A.Marina, and A.Contreras (2008).
Phosphorylation-independent activation of the atypical response regulator NblR.
  Microbiology, 154, 3002-3015.  
18353359 G.Wisedchaisri, M.Wu, D.R.Sherman, and W.G.Hol (2008).
Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation.
  J Mol Biol, 378, 227-242.
PDB codes: 3c3w 3c57
18366254 N.De, M.Pirruccello, P.V.Krasteva, N.Bae, R.V.Raghavan, and H.Sondermann (2008).
Phosphorylation-independent regulation of the diguanylate cyclase WspR.
  PLoS Biol, 6, e67.
PDB code: 3bre
18631241 R.Gao, Y.Tao, and A.M.Stock (2008).
System-level mapping of Escherichia coli response regulator dimerization with FRET hybrids.
  Mol Microbiol, 69, 1358-1372.  
18557815 S.A.Thomas, J.A.Brewster, and R.B.Bourret (2008).
Two variable active site residues modulate response regulator phosphoryl group stability.
  Mol Microbiol, 69, 453-465.  
18375564 S.J.Cariss, A.E.Tayler, and M.B.Avison (2008).
Defining the growth conditions and promoter-proximal DNA sequences required for activation of gene expression by CreBC in Escherichia coli.
  J Bacteriol, 190, 3930-3939.  
18436958 X.Wang, S.Bansal, M.Jiang, and J.H.Prestegard (2008).
RDC-assisted modeling of symmetric protein homo-oligomers.
  Protein Sci, 17, 899-907.  
18076904 X.Zhao, D.M.Copeland, A.S.Soares, and A.H.West (2008).
Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog.
  J Mol Biol, 375, 1141-1151.
PDB code: 2r25
17576598 D.Straume, M.Kjos, I.F.Nes, and D.B.Diep (2007).
Quorum-sensing based bacteriocin production is down-regulated by N-terminally truncated species of gene activators.
  Mol Genet Genomics, 278, 283-293.  
17491010 E.Hong, H.M.Lee, H.Ko, D.U.Kim, B.Y.Jeon, J.Jung, J.Shin, S.A.Lee, Y.Kim, Y.H.Jeon, C.Cheong, H.S.Cho, and W.Lee (2007).
Structure of an atypical orphan response regulator protein supports a new phosphorylation-independent regulatory mechanism.
  J Biol Chem, 282, 20667-20675.
PDB codes: 2hqn 2hqo 2hqr
17376070 G.Churchward (2007).
The two faces of Janus: virulence gene regulation by CovR/S in group A streptococci.
  Mol Microbiol, 64, 34-41.  
17942407 J.King-Scott, E.Nowak, E.Mylonas, S.Panjikar, M.Roessle, D.I.Svergun, and P.A.Tucker (2007).
The structure of a full-length response regulator from Mycobacterium tuberculosis in a stabilized three-dimensional domain-swapped, activated state.
  J Biol Chem, 282, 37717-37729.
PDB code: 2oqr
17511470 N.Friedland, T.R.Mack, M.Yu, L.W.Hung, T.C.Terwilliger, G.S.Waldo, and A.M.Stock (2007).
Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation.
  Biochemistry, 46, 6733-6743.
PDB code: 2gwr
17545283 P.Bachhawat, and A.M.Stock (2007).
Crystal structures of the receiver domain of the response regulator PhoP from Escherichia coli in the absence and presence of the phosphoryl analog beryllofluoride.
  J Bacteriol, 189, 5987-5995.
PDB codes: 2pkx 2pl1
17697997 P.Wassmann, C.Chan, R.Paul, A.Beck, H.Heerklotz, U.Jenal, and T.Schirmer (2007).
Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition.
  Structure, 15, 915-927.
PDB code: 2v0n
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
17433693 R.Gao, T.R.Mack, and A.M.Stock (2007).
Bacterial response regulators: versatile regulatory strategies from common domains.
  Trends Biochem Sci, 32, 225-234.  
17640875 R.Paul, S.Abel, P.Wassmann, A.Beck, H.Heerklotz, and U.Jenal (2007).
Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization.
  J Biol Chem, 282, 29170-29177.  
16788170 A.A.Gusa, J.Gao, V.Stringer, G.Churchward, and J.R.Scott (2006).
Phosphorylation of the group A Streptococcal CovR response regulator causes dimerization and promoter-specific recruitment by RNA polymerase.
  J Bacteriol, 188, 4620-4626.  
16929106 M.Solà, D.L.Drew, A.G.Blanco, F.X.Gomis-Rüth, and M.Coll (2006).
The cofactor-induced pre-active conformation in PhoB.
  Acta Crystallogr D Biol Crystallogr, 62, 1046-1057.
PDB code: 2iyn
16831870 S.Castang, S.Reverchon, P.Gouet, and W.Nasser (2006).
Direct evidence for the modulation of the activity of the Erwinia chrysanthemi quorum-sensing regulator ExpR by acylhomoserine lactone pheromone.
  J Biol Chem, 281, 29972-29987.  
16618701 T.Yoshida, L.Qin, L.A.Egger, and M.Inouye (2006).
Transcription regulation of ompF and ompC by a single transcription factor, OmpR.
  J Biol Chem, 281, 17114-17123.  
16322582 A.Toro-Roman, T.Wu, and A.M.Stock (2005).
A common dimerization interface in bacterial response regulators KdpE and TorR.
  Protein Sci, 14, 3077-3088.
PDB codes: 1zgz 1zh2 1zh4
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.