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PDBsum entry 1b00

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protein Protein-protein interface(s) links
Gene regulation PDB id
1b00
Jmol
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    
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.
122 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: 10.1006/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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20437037 I.Baca, D.Sprockett, and V.Dvornyk (2010).
Circadian input kinases and their homologs in cyanobacteria: evolutionary constraints versus architectural diversification.
  J Mol Evol, 70, 453-465.  
20171928 Y.J.Hsieh, and B.L.Wanner (2010).
Global regulation by the seven-component Pi signaling system.
  Curr Opin Microbiol, 13, 198-203.  
20826346 Z.Cheng, Y.W.He, S.C.Lim, R.Qamra, M.A.Walsh, L.H.Zhang, and H.Song (2010).
Structural basis of the sensor-synthase interaction in autoinduction of the quorum sensing signal DSF biosynthesis.
  Structure, 18, 1199-1209.
PDB codes: 3m6m 3m6n
19445950 E.S.Groban, E.J.Clarke, H.M.Salis, S.M.Miller, and C.A.Voigt (2009).
Kinetic buffering of cross talk between bacterial two-component sensors.
  J Mol Biol, 390, 380-393.  
19011915 J.Y.Song, E.S.Kim, D.W.Kim, S.E.Jensen, and K.J.Lee (2009).
A gene located downstream of the clavulanic acid gene cluster in Streptomyces clavuligerus ATCC 27064 encodes a putative response regulator that affects clavulanic acid production.
  J Ind Microbiol Biotechnol, 36, 301-311.  
19332669 S.Sun, A.Negrea, M.Rhen, and D.I.Andersson (2009).
Genetic analysis of colistin resistance in Salmonella enterica serovar Typhimurium.
  Antimicrob Agents Chemother, 53, 2298-2305.  
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.  
18065544 A.Sinha, S.Gupta, S.Bhutani, A.Pathak, and D.Sarkar (2008).
PhoP-PhoP interaction at adjacent PhoP binding sites is influenced by protein phosphorylation.
  J Bacteriol, 190, 1317-1328.  
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
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.  
16434396 E.Nowak, S.Panjikar, P.Konarev, D.I.Svergun, and P.A.Tucker (2006).
The structural basis of signal transduction for the response regulator PrrA from Mycobacterium tuberculosis.
  J Biol Chem, 281, 9659-9666.  
16816192 R.Gao, A.Mukhopadhyay, F.Fang, and D.G.Lynn (2006).
Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens.
  J Bacteriol, 188, 5204-5211.  
16717279 Z.C.Yuan, R.Zaheer, R.Morton, and T.M.Finan (2006).
Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria.
  Nucleic Acids Res, 34, 2686-2697.  
15882427 A.Sola-Landa, A.Rodríguez-García, E.Franco-Domínguez, and J.F.Martín (2005).
Binding of PhoP to promoters of phosphate-regulated genes in Streptomyces coelicolor: identification of PHO boxes.
  Mol Microbiol, 56, 1373-1385.  
16154092 P.Bachhawat, G.V.Swapna, G.T.Montelione, and A.M.Stock (2005).
Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states.
  Structure, 13, 1353-1363.
PDB code: 1zes
16154079 W.R.McCleary (2005).
No phobias about PhoB activation.
  Structure, 13, 1238-1239.  
15090529 C.J.Bent, N.W.Isaacs, T.J.Mitchell, and A.Riboldi-Tunnicliffe (2004).
Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states.
  J Bacteriol, 186, 2872-2879.
PDB codes: 1nxo 1nxp 1nxt 1nxw
15028686 H.Geng, S.Nakano, and M.M.Nakano (2004).
Transcriptional activation by Bacillus subtilis ResD: tandem binding to target elements and phosphorylation-dependent and -independent transcriptional activation.
  J Bacteriol, 186, 2028-2037.  
12486062 C.Birck, Y.Chen, F.M.Hulett, and J.P.Samama (2003).
The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface.
  J Bacteriol, 185, 254-261.
PDB code: 1mvo
12486069 D.Walthers, V.K.Tran, and L.J.Kenney (2003).
Interdomain linkers of homologous response regulators determine their mechanism of action.
  J Bacteriol, 185, 317-324.  
12614149 J.H.Zhang, G.Xiao, R.P.Gunsalus, and W.L.Hubbell (2003).
Phosphorylation triggers domain separation in the DNA binding response regulator NarL.
  Biochemistry, 42, 2552-2559.  
12702718 M.E.Castelli, A.Cauerhff, M.Amongero, F.C.Soncini, and E.G.Vescovi (2003).
The H box-harboring domain is key to the function of the Salmonella enterica PhoQ Mg2+-sensor in the recognition of its partner PhoP.
  J Biol Chem, 278, 23579-23585.  
12837793 V.L.Robinson, T.Wu, and A.M.Stock (2003).
Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily.
  J Bacteriol, 185, 4186-4194.
PDB code: 1p2f
12486063 Y.Chen, C.Birck, J.P.Samama, and F.M.Hulett (2003).
Residue R113 is essential for PhoP dimerization and function: a residue buried in the asymmetric PhoP dimer interface determined in the PhoPN three-dimensional crystal structure.
  J Bacteriol, 185, 262-273.  
12077136 K.Mattison, R.Oropeza, and L.J.Kenney (2002).
The linker region plays an important role in the interdomain communication of the response regulator OmpR.
  J Biol Chem, 277, 32714-32721.  
12123454 K.Yamamoto, H.Ogasawara, N.Fujita, R.Utsumi, and A.Ishihama (2002).
Novel mode of transcription regulation of divergently overlapping promoters by PhoP, the regulator of two-component system sensing external magnesium availability.
  Mol Microbiol, 45, 423-438.  
12381845 P.Roche, L.Mouawad, D.Perahia, J.P.Samama, and D.Kahn (2002).
Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101.
  Protein Sci, 11, 2622-2630.  
12067336 S.J.Stephenson, and M.Perego (2002).
Interaction surface of the Spo0A response regulator with the Spo0E phosphatase.
  Mol Microbiol, 44, 1455-1467.  
12176983 V.Guillet, N.Ohta, S.Cabantous, A.Newton, and J.P.Samama (2002).
Crystallographic and biochemical studies of DivK reveal novel features of an essential response regulator in Caulobacter crescentus.
  J Biol Chem, 277, 42003-42010.
PDB codes: 1m5t 1m5u 1mav 1mb0 1mb3
11847283 Y.J.Im, S.H.Rho, C.M.Park, S.S.Yang, J.G.Kang, J.Y.Lee, P.S.Song, and S.H.Eom (2002).
Crystal structure of a cyanobacterial phytochrome response regulator.
  Protein Sci, 11, 614-624.
PDB codes: 1i3c 1jlk
11244058 M.P.Allen, K.B.Zumbrennen, and W.R.McCleary (2001).
Genetic evidence that the alpha5 helix of the receiver domain of PhoB is involved in interdomain interactions.
  J Bacteriol, 183, 2204-2211.  
11134926 P.Gouet, N.Chinardet, M.Welch, V.Guillet, S.Cabantous, C.Birck, L.Mourey, and J.P.Samama (2001).
Further insights into the mechanism of function of the response regulator CheY from crystallographic studies of the CheY--CheA(124--257) complex.
  Acta Crystallogr D Biol Crystallogr, 57, 44-51.
PDB codes: 1ffg 1ffs 1ffw
10966457 A.M.Stock, V.L.Robinson, and P.N.Goudreau (2000).
Two-component signal transduction.
  Annu Rev Biochem, 69, 183-215.  
11073900 D.W.Ellison, and W.R.McCleary (2000).
The unphosphorylated receiver domain of PhoB silences the activity of its output domain.
  J Bacteriol, 182, 6592-6597.  
10613863 J.K.Cheung, and J.I.Rood (2000).
The VirR response regulator from Clostridium perfringens binds independently to two imperfect direct repeats located upstream of the pfoA promoter.
  J Bacteriol, 182, 57-66.  
10960104 J.Lee, J.T.Owens, I.Hwang, C.Meares, and S.Kustu (2000).
Phosphorylation-induced signal propagation in the response regulator ntrC.
  J Bacteriol, 182, 5188-5195.  
10837243 J.Stock, and S.Da Re (2000).
Signal transduction: response regulators on and off.
  Curr Biol, 10, R420-R424.  
10997904 J.Zapf, U.Sen, Madhusudan, J.A.Hoch, and K.I.Varughese (2000).
A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction.
  Structure, 8, 851-862.
PDB code: 1f51
10972837 X.Zhang, and F.M.Hulett (2000).
ResD signal transduction regulator of aerobic respiration in Bacillus subtilis: ctaA promoter regulation.
  Mol Microbiol, 37, 1208-1219.  
11053847 Y.J.Im, C.M.Park, J.I.Kim, S.S.Yang, J.G.Kang, S.H.Rho, J.I.Kim, W.K.Song, P.S.Song, and S.H.Eom (2000).
Crystallization and preliminary X-ray crystallographic studies of response regulator for cyanobacterial phytochrome, Rcp1.
  Acta Crystallogr D Biol Crystallogr, 56, 1446-1448.  
10417414 A.González, J.Pédelacq, M.Solà, F.X.Gomis-Rüth, M.Coll, J.Samama, and S.Benini (1999).
Two-wavelength MAD phasing: in search of the optimal choice of wavelengths.
  Acta Crystallogr D Biol Crystallogr, 55, 1449-1458.  
10647181 C.Birck, L.Mourey, P.Gouet, B.Fabry, J.Schumacher, P.Rousseau, D.Kahn, and J.P.Samama (1999).
Conformational changes induced by phosphorylation of the FixJ receiver domain.
  Structure, 7, 1505-1515.
PDB code: 1d5w
10611291 D.Yan, H.S.Cho, C.A.Hastings, M.M.Igo, S.Y.Lee, J.G.Pelton, V.Stewart, D.E.Wemmer, and S.Kustu (1999).
Beryllofluoride mimics phosphorylation of NtrC and other bacterial response regulators.
  Proc Natl Acad Sci U S A, 96, 14789-14794.  
10647185 H.J.Müller-Dieckmann, A.A.Grantz, and S.H.Kim (1999).
The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1.
  Structure, 7, 1547-1556.
PDB code: 1dcf
10647182 P.Gouet, B.Fabry, V.Guillet, C.Birck, L.Mourey, D.Kahn, and J.P.Samama (1999).
Structural transitions in the FixJ receiver domain.
  Structure, 7, 1517-1526.
PDB codes: 1dbw 1dck 1dcm
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.