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PDBsum entry 1u8t

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protein ligands Protein-protein interface(s) links
Signaling protein PDB id
1u8t
Jmol
Contents
Protein chains
126 a.a. *
13 a.a. *
Ligands
SO4 ×4
Waters ×568
* Residue conservation analysis
PDB id:
1u8t
Name: Signaling protein
Title: Crystal structure of chey d13k y106w alone and in complex with a flim peptide
Structure: Chemotaxis protein chey. Chain: a, b, c, d. Engineered: yes. Mutation: yes. Flagellar motor switch protein flim. Chain: e, f. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: chey. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: prepared using solid-state synthesis
Biol. unit: Monomer (from PQS)
Resolution:
1.50Å     R-factor:   0.200     R-free:   0.273
Authors: C.M.Dyer,M.L.Quillin,A.Campos,J.Lu,M.M.Mcevoy,A.C.Hausrath, E.M.Westbrook,P.Matsumura,B.W.Matthews,F.W.Dahlquist
Key ref:
C.M.Dyer et al. (2004). Structure of the constitutively active double mutant CheYD13K Y106W alone and in complex with a FliM peptide. J Mol Biol, 342, 1325-1335. PubMed id: 15351654 DOI: 10.1016/j.jmb.2004.07.084
Date:
06-Aug-04     Release date:   05-Oct-04    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AE67  (CHEY_ECOLI) -  Chemotaxis protein CheY
Seq:
Struc:
129 a.a.
126 a.a.*
Protein chains
Pfam   ArchSchema ?
P06974  (FLIM_ECOLI) -  Flagellar motor switch protein FliM
Seq:
Struc:
334 a.a.
13 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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: 10.1016/j.jmb.2004.07.084 J Mol Biol 342:1325-1335 (2004)
PubMed id: 15351654  
 
 
Structure of the constitutively active double mutant CheYD13K Y106W alone and in complex with a FliM peptide.
C.M.Dyer, M.L.Quillin, A.Campos, J.Lu, M.M.McEvoy, A.C.Hausrath, E.M.Westbrook, P.Matsumura, B.W.Matthews, F.W.Dahlquist.
 
  ABSTRACT  
 
CheY is a member of the response regulator protein superfamily that controls the chemotactic swimming response of motile bacteria. The CheY double mutant D13K Y106W (CheY**) is resistant to phosphorylation, yet is a highly effective mimic of phosphorylated CheY in vivo and in vitro. The conformational attributes of this protein that enable it to signal in a phosphorylation-independent manner are unknown. We have solved the crystal structure of selenomethionine-substituted CheY** in the presence of its target, a peptide (FliM16) derived from the flagellar motor switch, FliM, to 1.5A resolution with an R-factor of 19.6%. The asymmetric unit contains four CheY** molecules, two with FliM16 bound, and two without. The two CheY** molecules in the asymmetric unit that are bound to FliM16 adopt a conformation similar to BeF3- -activated wild-type CheY, and also bind FliM16 in a nearly identical manner. The CheY** molecules that do not bind FliM16 are found in a conformation similar to unphosphorylated wild-type CheY, suggesting that the active phenotype of this mutant is enabled by a facile interconversion between the active and inactive conformations. Finally, we propose a ligand-binding model for CheY and CheY**, in which Ile95 changes conformation in a Tyr/Trp106-dependent manner to accommodate FliM.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) The active site of CheY ** without FliM16 peptide bound. (b) The active site of CheY ** in complex with FliM16. The three water molecules that approximate the positions of the three fluoride moieties in BeF K 3 - activated wild-type CheY are shown in green. Red broken lines highlight interactions that are described in the text. (a) and (b) were generated with CheY ** chains D and B, respectively.
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (2004, 342, 1325-1335) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19943903 D.R.Buelow, and T.L.Raivio (2010).
Three (and more) component regulatory systems - auxiliary regulators of bacterial histidine kinases.
  Mol Microbiol, 75, 547-566.  
20207758 K.H.Lam, T.K.Ling, and S.W.Au (2010).
Crystal structure of activated CheY1 from Helicobacter pylori.
  J Bacteriol, 192, 2324-2334.
PDB codes: 3gwg 3h1e 3h1f 3h1g
19714199 B.A.Kidd, D.Baker, and W.E.Thomas (2009).
Computation of conformational coupling in allosteric proteins.
  PLoS Comput Biol, 5, e1000484.  
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.  
19246239 U.Jenal, and M.Y.Galperin (2009).
Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics.
  Curr Opin Microbiol, 12, 152-160.  
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
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
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.  
17488107 V.Vacic, C.J.Oldfield, A.Mohan, P.Radivojac, M.S.Cortese, V.N.Uversky, and A.K.Dunker (2007).
Characterization of molecular recognition features, MoRFs, and their binding partners.
  J Proteome Res, 6, 2351-2366.  
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
16475196 M.S.Formaneck, L.Ma, and Q.Cui (2006).
Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).
  Proteins, 63, 846-867.  
17019722 M.S.Formaneck, and Q.Cui (2006).
The use of a generalized born model for the analysis of protein conformational transitions: a comparative study with explicit solvent simulations for chemotaxis Y protein (CheY).
  J Comput Chem, 27, 1923-1943.  
16321923 K.I.Varughese (2005).
Conformational changes of Spo0F along the phosphotransfer pathway.
  J Bacteriol, 187, 8221-8227.  
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.