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PDBsum entry 1udr

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protein Protein-protein interface(s) links
Chemotaxis PDB id
1udr
Jmol
Contents
Protein chains
126 a.a. *
Waters ×224
* Residue conservation analysis
PDB id:
1udr
Name: Chemotaxis
Title: Chey mutant with lys 91 replaced by asp, lys 92 replaced by ala, ile 96 replaced by lys and ala 98 replaced by leu (stabilizing mutations in helix 4)
Structure: Chey protein. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. (Pharmacia)
Resolution:
1.90Å     R-factor:   0.189    
Authors: A.Parraga,M.Coll
Key ref:
M.Solà et al. (2000). Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY. J Mol Biol, 303, 213-225. PubMed id: 11023787 DOI: 10.1006/jmbi.2000.4507
Date:
05-Nov-96     Release date:   19-Nov-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AE67  (CHEY_ECOLI) -  Chemotaxis protein CheY
Seq:
Struc:
129 a.a.
126 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 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: 10.1006/jmbi.2000.4507 J Mol Biol 303:213-225 (2000)
PubMed id: 11023787  
 
 
Towards understanding a molecular switch mechanism: thermodynamic and crystallographic studies of the signal transduction protein CheY.
M.Solà, E.López-Hernández, P.Cronet, E.Lacroix, L.Serrano, M.Coll, A.Párraga.
 
  ABSTRACT  
 
The signal transduction protein CheY displays an alpha/beta-parallel polypeptide folding, including a highly unstable helix alpha4 and a strongly charged active site. Helix alpha4 has been shown to adopt various positions and conformations in different crystal structures, suggesting that it is a mobile segment. Furthermore, the instability of this helix is believed to have functional significance because it is involved in protein-protein contacts with the transmitter protein kinase CheA, the target protein FliM and the phosphatase CheZ. The active site of CheY comprises a cluster of three aspartic acid residues and a lysine residue, all of which participate in the binding of the Mg(2+) needed for the protein activation. Two steps were followed to study the activation mechanism of CheY upon phosphorylation: first, we independently substituted the three aspartic acid residues in the active site with alanine; second, several mutations were designed in helix alpha 4, both to increase its level of stability and to improve its packing against the protein core. The structural and thermodynamic analysis of these mutant proteins provides further evidence of the connection between the active-site area and helix alpha 4, and helps to understand how small movements at the active site are transmitted and amplified to the protein surface.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) Stereo diagram showing the superposition of D12A (green), D13A (blue), D57A (pink) over the apo-CheY structure (yellow; PDB entry 3CHY; [Volz and Matsumura 1991]). (b) Stereo representation of the area region around residue Leu98 in the mutant Hel43. Atoms interacting with the Leu98 side-chain are highlighted as spheres. The inner orientation of Tyr106 in the apo-CheY (PDB entry 3CHY; [Volz and Matsumura 1991]) is shown in darker thin bonds.
Figure 5.
Figure 5. (a) C^α tracing superimposition of mutant Hel43 (green) and apo-CheY (yellow; PDB entry 3CHY; [Volz and Matsumura 1991]). (b) Superposition of mutant Hel43 (green, with green labels) and apo-CheY (yellow, with red labels) at helix α4 and the preceding loop. (c) Skeletal and van der Waals representation of the region around residue 98 (blue spheres) in apo-CheY (PDB entry 3CHY; [Volz and Matsumura 1991]) and (d) in mutant Hel43 where alanine 98 has been replaced by a leucine residue.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 213-225) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20340133 H.Fu, G.Grimsley, J.M.Scholtz, and C.N.Pace (2010).
Increasing protein stability: importance of DeltaC(p) and the denatured state.
  Protein Sci, 19, 1044-1052.  
20735776 J.Herrou, R.Foreman, A.Fiebig, and S.Crosson (2010).
A structural model of anti-anti-σ inhibition by a two-component receiver domain: the PhyR stress response regulator.
  Mol Microbiol, 78, 290-304.
PDB code: 3n0r
21097705 M.T.Smith, J.Meissner, S.Esmonde, H.J.Wong, and E.M.Meiering (2010).
Energetics and mechanisms of folding and flipping the myristoyl switch in the {beta}-trefoil protein, hisactophilin.
  Proc Natl Acad Sci U S A, 107, 20952-20957.  
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.  
19646450 D.E.Kim, B.Blum, P.Bradley, and D.Baker (2009).
Sampling bottlenecks in de novo protein structure prediction.
  J Mol Biol, 393, 249-260.  
19399227 R.D.Hills, and C.L.Brooks (2009).
Insights from coarse-grained gō models for protein folding and dynamics.
  Int J Mol Sci, 10, 889-905.  
18298828 E.Kolmos, H.Schoof, M.Plümer, and S.J.Davis (2008).
Structural insights into the function of the core-circadian factor TIMING OF CAB2 EXPRESSION 1 (TOC1).
  J Circadian Rhythms, 6, 3.  
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.  
17523191 M.Bueno, C.J.Camacho, and J.Sancho (2007).
SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles.
  Proteins, 68, 850-862.  
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.  
15340927 A.J.Bordner, and R.A.Abagyan (2004).
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations.
  Proteins, 57, 400-413.  
12888490 T.J.Bollenbach, and D.B.Stern (2003).
Divalent metal-dependent catalysis and cleavage specificity of CSP41, a chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase superfamily.
  Nucleic Acids Res, 31, 4317-4325.  
12271440 J.Villanueva, V.Villegas, E.Querol, F.X.Avilés, and L.Serrano (2002).
Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
  J Mass Spectrom, 37, 974-984.  
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.  
11442836 E.Klauck, M.Lingnau, and R.Hengge-Aronis (2001).
Role of the response regulator RssB in sigma recognition and initiation of sigma proteolysis in Escherichia coli.
  Mol Microbiol, 40, 1381-1390.  
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 code is shown on the right.