PDBsum entry 2flk

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Signaling protein PDB id
Protein chains
128 a.a. *
13 a.a. *
CXS ×2
Waters ×80
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Crystal structure of chey in complex with chez(200-214) solv f432 crystal grown in caps (ph 10.5)
Structure: Chemotaxis protein chey. Chain: a. Engineered: yes. C-terminal 15-mer from chemotaxis protein chez. Chain: b. Fragment: residues 200-214. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 99287. Strain: lt2. Gene: chey. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence corresponds to thE C-terminal residues of the chez protein occurring naturally in salmone
Biol. unit: Hexamer (from PQS)
2.10Å     R-factor:   0.198     R-free:   0.207
Authors: J.Guhaniyogi,V.L.Robinson,A.M.Stock
Key ref:
J.Guhaniyogi et al. (2006). Crystal structures of beryllium fluoride-free and beryllium fluoride-bound CheY in complex with the conserved C-terminal peptide of CheZ reveal dual binding modes specific to CheY conformation. J Mol Biol, 359, 624-645. PubMed id: 16674976 DOI: 10.1016/j.jmb.2006.03.050
06-Jan-06     Release date:   23-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0A2D5  (CHEY_SALTY) -  Chemotaxis protein CheY
129 a.a.
128 a.a.
Protein chain
Pfam   ArchSchema ?
P07800  (CHEZ_SALTY) -  Protein phosphatase CheZ
214 a.a.
13 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     chemotaxis   3 terms 
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1016/j.jmb.2006.03.050 J Mol Biol 359:624-645 (2006)
PubMed id: 16674976  
Crystal structures of beryllium fluoride-free and beryllium fluoride-bound CheY in complex with the conserved C-terminal peptide of CheZ reveal dual binding modes specific to CheY conformation.
J.Guhaniyogi, V.L.Robinson, A.M.Stock.
Chemotaxis, the environment-specific swimming behavior of a bacterial cell is controlled by flagellar rotation. The steady-state level of the phosphorylated or activated form of the response regulator CheY dictates the direction of flagellar rotation. CheY phosphorylation is regulated by a fine equilibrium of three phosphotransfer activities: phosphorylation by the kinase CheA, its auto-dephosphorylation and dephosphorylation by its phosphatase CheZ. Efficient dephosphorylation of CheY by CheZ requires two spatially distinct protein-protein contacts: tethering of the two proteins to each other and formation of an active site for dephosphorylation. The former involves interaction of phosphorylated CheY with the small highly conserved C-terminal helix of CheZ (CheZ(C)), an indispensable structural component of the functional CheZ protein. To understand how the CheZ(C) helix, representing less than 10% of the full-length protein, ascertains molecular specificity of binding to CheY, we have determined crystal structures of CheY in complex with a synthetic peptide corresponding to 15 C-terminal residues of CheZ (CheZ(200-214)) at resolutions ranging from 2.0 A to 2.3A. These structures provide a detailed view of the CheZ(C) peptide interaction both in the presence and absence of the phosphoryl analog, BeF3-. Our studies reveal that two different modes of binding the CheZ(200-214) peptide are dictated by the conformational state of CheY in the complex. Our structures suggest that the CheZ(C) helix binds to a "meta-active" conformation of inactive CheY and it does so in an orientation that is distinct from the one in which it binds activated CheY. Our dual binding mode hypothesis provides implications for reverse information flow in CheY and extends previous observations on inherent resilience in CheY-like signaling domains.
  Selected figure(s)  
Figure 3.
Figure 3. The CheZ[200-214] peptide-CheY interface. Ribbon representation of (a) the F432YZ[200-214] interface and (b) the P2(1)2(1)2YZ[200-214] interface. The side-chains of key contacting residues are illustrated as ball and stick models and hydrophobic contacts are shown as green patches. (c) Relative B-factors of CheZ[200-214] in the CheY-CheZ[200-214] structures. The relative B-factor versus CheZ residue number plot in Click to view the MathML source- [0?wchp=dGLbVlb-zSkzk] -free F432YZ[200-214] is shown in cyan, that in Click to view the MathML source- [0?wchp=dGLbVlb-zSkzk] -bound F432YZ[200-214] in deep blue and that in Click to view the MathML source- [0?wchp=dGLbVlb-zSkzk] -bound P2(1)2(1)2YZ[200-214] in orange. B[residue] is the overall B-factor for each residue and B[CheZ] is the overall B-factor for all atoms of CheZ[200-214] included in the final model. (d) Schematic representation of the CheY-CheZ[200-214] contacts. The F432Z[200-214] primary sequence in cyan and the P2(1)2(1)2Z[200-214] primary sequence in orange are shown on either side of the C-terminal half of CheY, represented in secondary structural elements. Participating residues are highlighted. Hydrophobic contacts are illustrated as continuous grey lines, salt bridges as broken black lines and hydrogen bonds as continuous black lines. The Click to view the MathML source- [0?wchp=dGLbVlb-zSkzk] -free and Click to view the MathML source- [0?wchp=dGLbVlb-zSkzk] -bound F432YZ[200-214] structures solved from crystals grown in Tris (pH 8.4) are used as representatives of F432YZ[200-214] structures in this Figure.
Figure 4.
Figure 4. Ribbon diagrams of CheY-CheZ[C] structures upon superposition of CheY showing different orientations of CheZ[C]. CheY molecules in F432YZ[200-214], P2(1)2(1)2YZ[200-214] and CheY-CheZ[1-214]15 structures are shown in light gray and the respective CheZ[C] helices are shown in cyan, orange and magenta, respectively. The Click to view the MathML source- [0?wchp=dGLbVlb-zSkzk] -free F432YZ[200-214] structure solved from a crystal grown in Tris (pH 8.4) is used in this Figure as a representative of all six F432YZ[200-214] structures.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 624-645) copyright 2006.  
  Figures were 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
20133180 R.E.Silversmith (2010).
Auxiliary phosphatases in two-component signal transduction.
  Curr Opin Microbiol, 13, 177-183.  
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.  
18045868 A.R.Diaz, S.Stephenson, J.M.Green, V.M.Levdikov, A.J.Wilkinson, and M.Perego (2008).
Functional Role for a Conserved Aspartate in the Spo0E Signature Motif Involved in the Dephosphorylation of the Bacillus subtilis Sporulation Regulator Spo0A.
  J Biol Chem, 283, 2962-2972.  
18083806 J.Guhaniyogi, T.Wu, S.S.Patel, and A.M.Stock (2008).
Interaction of CheY with the C-terminal peptide of CheZ.
  J Bacteriol, 190, 1419-1428.
PDB codes: 2pl9 2pmc
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
17998207 R.E.Silversmith, M.D.Levin, E.Schilling, and R.B.Bourret (2008).
Kinetic characterization of catalysis by the chemotaxis phosphatase CheZ. Modulation of activity by the phosphorylated CheY substrate.
  J Biol Chem, 283, 756-765.  
17573816 J.S.Fraser, J.P.Merlie, N.Echols, S.R.Weisfield, T.Mignot, D.E.Wemmer, D.R.Zusman, and T.Alber (2007).
An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
  Mol Microbiol, 65, 319-332.
PDB codes: 2gkg 2i6f 2nt3 2nt4
17084862 M.Musial-Siwek, S.L.Rusch, and D.A.Kendall (2007).
Selective photoaffinity labeling identifies the signal peptide binding domain on SecA.
  J Mol Biol, 365, 637-648.  
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.  
17050920 A.M.Stock, and J.Guhaniyogi (2006).
A new perspective on response regulator activation.
  J Bacteriol, 188, 7328-7330.  
17050923 C.M.Dyer, and F.W.Dahlquist (2006).
Switched or not?: the structure of unphosphorylated CheY bound to the N terminus of FliM.
  J Bacteriol, 188, 7354-7363.
PDB code: 2b1j
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.