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PDBsum entry 1djm

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protein links
Signaling protein PDB id
1djm
Jmol
Contents
Protein chain
129 a.a. *
* Residue conservation analysis
PDB id:
1djm
Name: Signaling protein
Title: Solution structure of bef3-activated chey from escherichia coli
Structure: Chemotaxis protein y. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 27 models
Authors: H.S.Cho,S.Y.Lee,D.Yan,X.Pan,J.S.Parkinson,S.Kustu, D.E.Wemmer,J.G.Pelton
Key ref:
H.S.Cho et al. (2000). NMR structure of activated CheY. J Mol Biol, 297, 543-551. PubMed id: 10731410 DOI: 10.1006/jmbi.2000.3595
Date:
03-Dec-99     Release date:   05-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AE67  (CHEY_ECOLI) -  Chemotaxis protein CheY
Seq:
Struc:
129 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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.2000.3595 J Mol Biol 297:543-551 (2000)
PubMed id: 10731410  
 
 
NMR structure of activated CheY.
H.S.Cho, S.Y.Lee, D.Yan, X.Pan, J.S.Parkinson, S.Kustu, D.E.Wemmer, J.G.Pelton.
 
  ABSTRACT  
 
The CheY protein is the response regulator in bacterial chemotaxis. Phosphorylation of a conserved aspartyl residue induces structural changes that convert the protein from an inactive to an active state. The short half-life of the aspartyl-phosphate has precluded detailed structural analysis of the active protein. Persistent activation of Escherichia coli CheY was achieved by complexation with beryllofluoride (BeF(3)(-)) and the structure determined by NMR spectroscopy to a backbone r.m.s.d. of 0.58(+/-0.08) A. Formation of a hydrogen bond between the Thr87 OH group and an active site acceptor, presumably Asp57.BeF(3)(-), stabilizes a coupled rearrangement of highly conserved residues, Thr87 and Tyr106, along with displacement of beta4 and H4, to yield the active state. The coupled rearrangement may be a more general mechanism for activation of receiver domains.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (a) 15N-1H FHSQC spectrum of BeF[3]-CheY along with (b) superpositions of backbone N, C^a, and C' coordinates for BeF[3]-activated CheY and (c) comparison of BeF[3]-activated and inactive CheY structures shown in stereoview. (a) In the FHSQC, spectrum peaks are labeled with residue numbers. Unassigned backbone resonances are labeled UA. Pairs of side-chain NH[2] resonances are connected by horizontal lines. Signals enclosed in boxes are folded in the 15N dimension. (b) The 27 structures of BeF[3]-activated CheY. Backbone coordinates for residues in the five helices and five-stranded b-sheet were superimposed. (c) Superposition of the 27 structures of BeF[3]-activated CheY (blue), with apo X-ray [Volz and Matsumura 1991] (gold), magnesium-bound X-ray [Bellsolell et al 1994] (red), and mean magnesium-bound NMR [Moy et al 1994] (magenta) structures. Superposition included backbone coordinates for residues in H1, H2, b1, b2, and b3. Considering the mean coordinates obtained from the family of magnesium-bound [Moy et al 1994] and BeF[3]-activated NMR structures, backbone superposition of H1, H2, b1, b2, and b3 yields an r.m.s.d. value of 2.4 Å for the backbone coodinates of residues in H3, b4, H4, b5, and H5. The Figure was produced with the program MOLMOL [Koradi et al 1996]. Uniformly 15N and 15N/13C-labeled samples were prepared by growth in M9 minimal medium supplemented with biotin and either [15N]ammonium chloride or [15N]ammonium chloride and [13C]glucose. The BeF[3]-activated sample conditions were 4 mM CheY, 16 mM BeCl[2], 100 mM NaF, 20 mM MgCl[2], at pH 6.7, and 10 % 2H[2]O. NMR spectra were recorded on AMX 600 and DRX 500 NMR spectrometers at 25 °C. Backbone resonances were assigned with 3D 15N NOESY-FHSQC [Talluri and Wagner 1996], HNCACB [Wittekind and Mueller 1993], CBCA(CO)NH [Grzesiek and Bax 1992a], and HNCA [Grzesiek and Bax 1992b] spectra. Side-chain aliphatic 13C/1H pairs were assigned with 3D 15N TOCSY-HSQC [Driscoll et al 1990], HCCH-TOCSY [Kay et al 1993] and CBCA(CO)NH spectra. In each of the experiments above, purge-type pulsed-field gradients were used to suppress artifacts and the solvent signal [Bax and Pochapsky 1992]. Aromatic assignments were obtained from DQF-COSY [Rance et al 1983] and 13C/1H HMQC spectra [Bax et al 1990]. The assignment process was also aided by making reference to published chemical shifts for CheY [Bruix et al 1993 and Moy et al 1994]. Phi torsion angle restraints were obtained from a 15N HMQC-J spectrum [Kay and Bax 1990]. Stereospecific assignments for Val and Leu methyl groups were obtained by comparison of ct-HSQC spectra of uniformly 13C-labeled and 10 % uniformly 13C-labeled samples [Neri et al 1989 and Szyperski et al 1992]. x1 restraints for the Val, Ile, and Thr residues were obtained from ct-HMQC-J spectra [Grzesiek et al 1993 and Vuister et al 1993a]. NOEs identified in 3D NOESY-FHSQC, 4D 13C/15N HMQC-NOESY-FHSQC and 4D 13C/13C HMQC-NOESY-HMQC (all recorded with a 100 ms mixing time) [Vuister et al 1993b] spectra were classified as strong (2.9 Å upper distance limit), medium (3.3 Å), or weak (5.0 Å). A total of 972 non-trivial NOE restraints (213 intraresidue, 271 sequential, 238 medium-range, and 250 long-range) were used as input to DYANA [Guntert et al 1997], along with 78 phi torsion angle restraints and 17 x1 restraints for the Val, Ile, and Thr residues. Once sets of 20 (of 60) structures reached a backbone r.m.s.d. of 1 Å, 47 hydrogen bonds (94 upper and 94 lower distance restraints (H-O distance restraint 1.8-2.0 Å; N-O 2.7-3.0 Å)), identified on the basis of slow amide proton exchange rates (protection factors greater than 75) and short donor/acceptor distances were included in the calculations. Structures resulting from DYANA calculations with a pseudoatom (van der Waals radius 2.5 Å) corresponding to BeF[3]^ - attached to the side-chain of Asp57 resulted in a backbone r.m.s.d. value of only 0.4 Å when compared to structures without the additional pseudoatom. The 27 of 60 structures (BeF[3]^ - pseudoatom not included) with residual target function values less than 1.0 Å2 (Table 1; target function before energy minimization was 0.3(±0.2) Å2) were subjected to restrained energy minimization using the AMBER94 forcefield [Cornell et al 1995] implemented in the program OPAL [Luginbuhl et al 1996]. Conjugate gradient minimization (1500 steps) included bond, angle, dihedral, improper dihedral, van der Waals, electrostatic, NMR distance, and NMR torsion angle terms. The minimization was performed in a shell of water at least 6 Å thick, with the dielectric constant set to 1, and with no cut-off for non-bonded interactions. PROCHECK analysis [Laskowski et al 1993] of the structures revealed that 99 % of the residues fall within the allowed or generously allowed regions of the Ramachandran map. The 27 energy-minimized structures are used to represent the solution structure of CheY complexed with beryllofluoride and magnesium.
Figure 3.
Figure 3. Ribbon diagrams of CheY in stereo showing movement of side-chains Thr87 and Tyr106 upon activation. Superposition included backbone coordinates for residues in H1, H2, b1, b2, and b3. Relative that depicted in Figure 2, the structures are rotated 90° about a horizontal axis in the page, affording a view (top) of the active site. The loops between b3 and H3 and between H3 and b4 are ill-defined by the NMR data, and should not be used for comparison. (a) CheY taken from the inactive magnesium-bound NMR structure [Moy et al 1994] and (b) representative NMR structure of BeF[3]-activated CheY. Asp57 (blue) is the site of phosphorylation. Highly conserved Tyr106 (green) and Thr87 (red) are also shown. The Thr87 hydroxyl group is represented by a small ball. BeF[3]^ - is modeled as a black ball attached to Asp57. The Figure was created with the program MOLSCRIPT [Kraulis 1991].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 543-551) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21456702 K.Itoh, and M.Sasai (2011).
Statistical mechanics of protein allostery: roles of backbone and side-chain structural fluctuations.
  J Chem Phys, 134, 125102.  
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
19376848 F.Rao, Y.Qi, H.S.Chong, M.Kotaka, B.Li, J.Li, J.Lescar, K.Tang, and Z.X.Liang (2009).
The functional role of a conserved loop in EAL domain-based cyclic di-GMP-specific phosphodiesterase.
  J Bacteriol, 191, 4722-4731.  
19304952 X.J.He, K.E.Mulford, and J.S.Fassler (2009).
Oxidative stress function of the Saccharomyces cerevisiae Skn7 receiver domain.
  Eukaryot Cell, 8, 768-778.  
18353359 G.Wisedchaisri, M.Wu, D.R.Sherman, and W.G.Hol (2008).
Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation.
  J Mol Biol, 378, 227-242.
PDB codes: 3c3w 3c57
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
18560010 Q.Cui, and M.Karplus (2008).
Allostery and cooperativity revisited.
  Protein Sci, 17, 1295-1307.  
17576598 D.Straume, M.Kjos, I.F.Nes, and D.B.Diep (2007).
Quorum-sensing based bacteriocin production is down-regulated by N-terminally truncated species of gene activators.
  Mol Genet Genomics, 278, 283-293.  
17586650 E.A.Hussa, T.M.O'Shea, C.L.Darnell, E.G.Ruby, and K.L.Visick (2007).
Two-component response regulators of Vibrio fischeri: identification, mutagenesis, and characterization.
  J Bacteriol, 189, 5825-5838.  
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.  
17050920 A.M.Stock, and J.Guhaniyogi (2006).
A new perspective on response regulator activation.
  J Bacteriol, 188, 7328-7330.  
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.  
16882724 S.Y.Park, B.Lowder, A.M.Bilwes, D.F.Blair, and B.R.Crane (2006).
Structure of FliM provides insight into assembly of the switch complex in the bacterial flagella motor.
  Proc Natl Acad Sci U S A, 103, 11886-11891.
PDB code: 2hp7
15808745 K.Stephenson, and R.J.Lewis (2005).
Molecular insights into the initiation of sporulation in Gram-positive bacteria: new technologies for an old phenomenon.
  FEMS Microbiol Rev, 29, 281-301.  
15741343 T.J.Lowery, M.Doucleff, E.J.Ruiz, S.M.Rubin, A.Pines, and D.E.Wemmer (2005).
Distinguishing multiple chemotaxis Y protein conformations with laser-polarized 129Xe NMR.
  Protein Sci, 14, 848-855.
PDB code: 1zdm
15573139 G.H.Wadhams, and J.P.Armitage (2004).
Making sense of it all: bacterial chemotaxis.
  Nat Rev Mol Cell Biol, 5, 1024-1037.  
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.  
14555659 Y.Kim, A.F.Yakunin, E.Kuznetsova, X.Xu, M.Pennycooke, J.Gu, F.Cheung, M.Proudfoot, C.H.Arrowsmith, A.Joachimiak, A.M.Edwards, and D.Christendat (2004).
Structure- and function-based characterization of a new phosphoglycolate phosphatase from Thermoplasma acidophilum.
  J Biol Chem, 279, 517-526.
PDB code: 1l6r
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
12824492 D.H.Shin, A.Roberts, J.Jancarik, H.Yokota, R.Kim, D.E.Wemmer, and S.H.Kim (2003).
Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima.
  Protein Sci, 12, 1464-1472.
PDB code: 1nf2
14563873 J.G.Smith, J.A.Latiolais, G.P.Guanga, S.Citineni, R.E.Silversmith, and R.B.Bourret (2003).
Investigation of the role of electrostatic charge in activation of the Escherichia coli response regulator CheY.
  J Bacteriol, 185, 6385-6391.  
12586392 R.E.Marquis, S.A.Clock, and M.Mota-Meira (2003).
Fluoride and organic weak acids as modulators of microbial physiology.
  FEMS Microbiol Rev, 26, 493-510.  
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.  
11406410 A.H.West, and A.M.Stock (2001).
Histidine kinases and response regulator proteins in two-component signaling systems.
  Trends Biochem Sci, 26, 369-376.  
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.  
11438683 H.Cho, W.Wang, R.Kim, H.Yokota, S.Damo, S.H.Kim, D.Wemmer, S.Kustu, and D.Yan (2001).
BeF(3)(-) acts as a phosphate analog in proteins phosphorylated on aspartate: structure of a BeF(3)(-) complex with phosphoserine phosphatase.
  Proc Natl Acad Sci U S A, 98, 8525-8530.
PDB code: 1j97
11528005 L.L.McCarter (2001).
Polar flagellar motility of the Vibrionaceae.
  Microbiol Mol Biol Rev, 65, 445.  
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.  
11353835 M.Schuster, R.E.Silversmith, and R.B.Bourret (2001).
Conformational coupling in the chemotaxis response regulator CheY.
  Proc Natl Acad Sci U S A, 98, 6003-6008.  
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
11669626 R.L.Saxl, G.S.Anand, and A.M.Stock (2001).
Synthesis and biochemical characterization of a phosphorylated analogue of the response regulator CheB.
  Biochemistry, 40, 12896-12903.  
11169108 T.Fuchs, P.Wiget, M.Osterås, and U.Jenal (2001).
Precise amounts of a novel member of a phosphotransferase superfamily are essential for growth and normal morphology in Caulobacter crescentus.
  Mol Microbiol, 39, 679-692.  
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.  
11069648 R.J.Lewis, S.Krzywda, J.A.Brannigan, J.P.Turkenburg, K.Muchová, E.J.Dodson, I.Barák, and A.J.Wilkinson (2000).
The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography.
  Mol Microbiol, 38, 198-212.
PDB code: 1fc3
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.