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PDBsum entry 6chy

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protein ligands Protein-protein interface(s) links
Signal transduction protein PDB id
6chy
Jmol
Contents
Protein chains
128 a.a. *
Ligands
SO4
Waters ×177
* Residue conservation analysis
PDB id:
6chy
Name: Signal transduction protein
Title: Structure of chemotaxis protein chey
Structure: Chey. Chain: a, b. Engineered: yes. Mutation: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.33Å     R-factor:   0.185    
Authors: X.Zhu,J.Rebello,P.Matsumura,K.Volz
Key ref:
X.Zhu et al. (1997). Crystal structures of CheY mutants Y106W and T87I/Y106W. CheY activation correlates with movement of residue 106. J Biol Chem, 272, 5000-5006. PubMed id: 9030562 DOI: 10.1074/jbc.272.38.23758
Date:
29-Aug-96     Release date:   07-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AE67  (CHEY_ECOLI) -  Chemotaxis protein CheY
Seq:
Struc:
129 a.a.
128 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     intracellular signal transduction   7 terms 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1074/jbc.272.38.23758 J Biol Chem 272:5000-5006 (1997)
PubMed id: 9030562  
 
 
Crystal structures of CheY mutants Y106W and T87I/Y106W. CheY activation correlates with movement of residue 106.
X.Zhu, J.Rebello, P.Matsumura, K.Volz.
 
  ABSTRACT  
 
Position 106 in CheY is highly conserved as an aromatic residue in the response regulator superfamily. In the structure of the wild-type, apo-CheY, Tyr106 is a rotamer whose electron density is observed in both the inside and the outside positions. In the structure of the T87I mutant of CheY, the threonine to isoleucine change at position 87 causes the side chain of Tyr106 to be exclusively restricted to the outside position. In this report we demonstrate that the T87I mutation causes cells to be smooth swimming and non-chemotactic. We also show that another CheY mutant, Y106W, causes cells to be more tumbly than wild-type CheY, and impairs chemotaxis. In the structure of Y106W, the side chain of Trp106 stays exclusively in the inside position. Furthermore, a T87I/Y106W double mutant, which confers the same phenotype as T87I, restricts the side chain of Trp106 to the outside position. The results from these behavioral and structural studies indicate that the rotameric nature of the Tyr106 residue is involved in activation of the CheY molecule. Specifically, CheY's signaling ability correlates with the conformational heterogeneity of the Tyr106 side chain. Our data also suggest that these mutations affect the signal at an event subsequent to phosphorylation.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Flagellar rotation bias of cells with either wild-type or mutant cheY. Tethered cells that were actively spinning were^ videotaped through a light microscope within a 30-min period. The flagellar rotations of each cell was quantitated for 10 continuous s. More than 100 tethered cells were analyzed for each sample. The flagellar rotation biases were classified into five different categories: exclusive counterclockwise rotation (CCW), counterclockwise^ bias with rotation reversals (CCW-R), rotation reversals with no bias direction (R), clockwise bias with rotation reversals (CW-R), or exclusive clockwise rotation (CW). The strains were^ the same as described in Fig. 1.
Figure 4.
Fig. 4. Stereo diagrams of the structural differences at position 106. Panel A, wild-type CheY (10); panel B, T87I (17); panel C, Y106W (this work); and panel D, T87I/Y106W (this work). The solvent accessible surface for each molecule was calculated^ with residue 106 modeled as a glycine for visualization of the^ different cavity volumes. Electron density from an |F[o] F[c]| [calc] omit map of the 106 side chain for each of^ the structures is shown, contoured at 3 . The orientations in the panels are approximately the same, with minor rotations to optimize viewing.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 5000-5006) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20859643 P.V.Attwood, P.G.Besant, and M.J.Piggott (2011).
Focus on phosphoaspartate and phosphoglutamate.
  Amino Acids, 40, 1035-1051.  
20226790 R.D.Hills, S.V.Kathuria, L.A.Wallace, I.J.Day, C.L.Brooks, and C.R.Matthews (2010).
Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.
  J Mol Biol, 398, 332-350.  
18718017 K.Chourey, W.Wei, X.F.Wan, and D.K.Thompson (2008).
Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge.
  BMC Genomics, 9, 395.  
18801331 K.McAdams, E.S.Casper, R.Matthew Haas, B.D.Santarsiero, A.L.Eggler, A.Mesecar, and C.J.Halkides (2008).
The structures of T87I phosphono-CheY and T87I/Y106W phosphono-CheY help to explain their binding affinities to the FliM and CheZ peptides.
  Arch Biochem Biophys, 479, 105-113.
PDB codes: 2id7 2id9 2idm
18644380 R.D.Hills, and C.L.Brooks (2008).
Subdomain competition, cooperativity, and topological frustration in the folding of CheY.
  J Mol Biol, 382, 485-495.  
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
17655236 L.Ma, and Q.Cui (2007).
Activation mechanism of a signaling protein at atomic resolution from advanced computations.
  J Am Chem Soc, 129, 10261-10268.  
17172298 M.H.Knaggs, F.R.Salsbury, M.H.Edgell, and J.S.Fetrow (2007).
Insights into correlated motions and long-range interactions in CheY derived from molecular dynamics simulations.
  Biophys J, 92, 2062-2079.  
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
17050920 A.M.Stock, and J.Guhaniyogi (2006).
A new perspective on response regulator activation.
  J Bacteriol, 188, 7328-7330.  
16321923 K.I.Varughese (2005).
Conformational changes of Spo0F along the phosphotransfer pathway.
  J Bacteriol, 187, 8221-8227.  
15262956 A.Ferré, J.De La Mora, T.Ballado, L.Camarena, and G.Dreyfus (2004).
Biochemical study of multiple CheY response regulators of the chemotactic pathway of Rhodobacter sphaeroides.
  J Bacteriol, 186, 5172-5177.  
15187186 H.Szurmant, and G.W.Ordal (2004).
Diversity in chemotaxis mechanisms among the bacteria and archaea.
  Microbiol Mol Biol Rev, 68, 301-319.  
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.  
12381847 S.Da Re, T.Tolstykh, P.M.Wolanin, and J.B.Stock (2002).
Genetic analysis of response regulator activation in bacterial chemotaxis suggests an intermolecular mechanism.
  Protein Sci, 11, 2644-2654.  
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
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
11092844 A.Bren, and M.Eisenbach (2000).
How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation.
  J Bacteriol, 182, 6865-6873.  
10966457 A.M.Stock, V.L.Robinson, and P.N.Goudreau (2000).
Two-component signal transduction.
  Annu Rev Biochem, 69, 183-215.  
10837243 J.Stock, and S.Da Re (2000).
Signal transduction: response regulators on and off.
  Curr Biol, 10, R420-R424.  
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
10393292 M.Kato, T.Shimizu, T.Mizuno, and T.Hakoshima (1999).
Structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor protein ArcB complexed with the chemotaxis response regulator CheY.
  Acta Crystallogr D Biol Crystallogr, 55, 1257-1263.
PDB code: 1bdj
  9657998 J.L.Appleby, and R.B.Bourret (1998).
Proposed signal transduction role for conserved CheY residue Thr87, a member of the response regulator active-site quintet.
  J Bacteriol, 180, 3563-3569.  
9651669 M.Eisenbach, and S.R.Caplan (1998).
Bacterial chemotaxis: unsolved mystery of the flagellar switch.
  Curr Biol, 8, R444-R446.  
9636149 M.M.McEvoy, A.C.Hausrath, G.B.Randolph, S.J.Remington, and F.W.Dahlquist (1998).
Two binding modes reveal flexibility in kinase/response regulator interactions in the bacterial chemotaxis pathway.
  Proc Natl Acad Sci U S A, 95, 7333-7338.
PDB code: 1eay
9535095 M.Schuster, W.N.Abouhamad, R.E.Silversmith, and R.B.Bourret (1998).
Chemotactic response regulator mutant CheY95IV exhibits enhanced binding to the flagellar switch and phosphorylation-dependent constitutive signalling.
  Mol Microbiol, 27, 1065-1075.  
10089524 M.Staley, L.C.Zeringue, R.D.Kidd, B.T.Nixon, and G.K.Farber (1998).
Crystallization and preliminary X-ray studies of the Rhizobium meliloti DctD two-component receiver domain.
  Acta Crystallogr D Biol Crystallogr, 54, 1416-1418.  
9437425 M.Welch, N.Chinardet, L.Mourey, C.Birck, and J.P.Samama (1998).
Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY.
  Nat Struct Biol, 5, 25-29.
PDB code: 1a0o
10066483 P.N.Goudreau, and A.M.Stock (1998).
Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling.
  Curr Opin Microbiol, 1, 160-169.  
9560203 R.Ramakrishnan, M.Schuster, and R.B.Bourret (1998).
Acetylation at Lys-92 enhances signaling by the chemotaxis response regulator protein CheY.
  Proc Natl Acad Sci U S A, 95, 4918-4923.  
9465023 S.Djordjevic, P.N.Goudreau, Q.Xu, A.M.Stock, and A.H.West (1998).
Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain.
  Proc Natl Acad Sci U S A, 95, 1381-1386.
PDB code: 1a2o
9540996 V.A.Feher, Y.L.Tzeng, J.A.Hoch, and J.Cavanagh (1998).
Identification of communication networks in Spo0F: a model for phosphorylation-induced conformational change and implications for activation of multiple domain bacterial response regulators.
  FEBS Lett, 425, 1-6.  
9254596 V.A.Feher, J.W.Zapf, J.A.Hoch, J.M.Whiteley, L.P.McIntosh, M.Rance, N.J.Skelton, F.W.Dahlquist, and J.Cavanagh (1997).
High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition.
  Biochemistry, 36, 10015-10025.
PDB codes: 1fsp 2fsp
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.