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PDBsum entry 1f4v

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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
1f4v
Jmol
Contents
Protein chains
128 a.a. *
16 a.a. *
14 a.a. *
Ligands
BEF ×3
GOL ×2
Metals
_MG ×3
Waters ×280
* Residue conservation analysis
PDB id:
1f4v
Name: Signaling protein
Title: Crystal structure of activated chey bound to the n-terminus
Structure: Chemotaxis chey protein. Chain: a, b, c. Engineered: yes. Flagellar motor switch protein. Chain: d, e, f. Fragment: n-terminus. Synonym: flim
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Organism_taxid: 562
Biol. unit: Dodecamer (from PQS)
Resolution:
2.22Å     R-factor:   0.217     R-free:   0.258
Authors: S.Y.Lee,H.S.Cho,J.G.Pelton,D.Yan,R.K.Henderson,D.King,L.S.Hu S.Kustu,E.A.Berry,D.E.Wemmer
Key ref:
S.Y.Lee et al. (2001). Crystal structure of an activated response regulator bound to its target. Nat Struct Biol, 8, 52-56. PubMed id: 11135671 DOI: 10.1038/83053
Date:
10-Jun-00     Release date:   17-Jan-01    
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.
Protein chain
Pfam   ArchSchema ?
P06974  (FLIM_ECOLI) -  Flagellar motor switch protein FliM
Seq:
Struc:
334 a.a.
16 a.a.
Protein chains
Pfam   ArchSchema ?
P06974  (FLIM_ECOLI) -  Flagellar motor switch protein FliM
Seq:
Struc:
334 a.a.
14 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: 10.1038/83053 Nat Struct Biol 8:52-56 (2001)
PubMed id: 11135671  
 
 
Crystal structure of an activated response regulator bound to its target.
S.Y.Lee, H.S.Cho, J.G.Pelton, D.Yan, R.K.Henderson, D.S.King, L.Huang, S.Kustu, E.A.Berry, D.E.Wemmer.
 
  ABSTRACT  
 
The chemotactic regulator CheY controls the direction of flagellar rotation in Escherichia coli. We have determined the crystal structure of BeF3--activated CheY from E. coli in complex with an N-terminal peptide derived from its target, FliM. The structure reveals that the first seven residues of the peptide pack against the beta4-H4 loop and helix H4 of CheY in an extended conformation, whereas residues 8-15 form two turns of helix and pack against the H4-beta5-H5 face. The peptide binds the only region of CheY that undergoes noticeable conformational change upon activation and would most likely be sandwiched between activated CheY and the remainder of FliM to reverse the direction of flagellar rotation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo view of the active site of CheY showing the F[o] - F[c] electron density for the BeF[3]^- moiety contoured at 5.5 . This map was calculated with the occupancy of the BeF[3]^- moiety set to zero. The three F atoms, shown in light blue, adopt a tetrahedral geometry around Be and hydrogen bond with the hydroxyl group of Thr 87, N of Lys 109 and backbone amides of Ala 88 and Asn 59. BeF[3]^- also serves as a ligand for Mg2+ (dark green). The two water molecules that coordinate with Mg2+ are shown in red. Carbon, nitrogen, and oxygen atoms are shown in green, dark blue, and red, respectively. For additional interactions see the text.
Figure 3.
Figure 3. GRASP33 electrostatic surface representations of: a, apo-CheY with Tyr 106 in the solvent exposed position34; b, CheY alone from the CheY -N16-FliM complex; c, the CheY -N16-FliM complex. Comparison of (a) and (b) shows that Tyr 106 in the solvent exposed position sterically interferes with peptide binding to the H4- 5-H5 face.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 52-56) copyright 2001.  
  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.  
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
20439729 M.K.Sarkar, K.Paul, and D.Blair (2010).
Chemotaxis signaling protein CheY binds to the rotor protein FliN to control the direction of flagellar rotation in Escherichia coli.
  Proc Natl Acad Sci U S A, 107, 9370-9375.  
19858188 M.K.Sarkar, K.Paul, and D.F.Blair (2010).
Subunit organization and reversal-associated movements in the flagellar switch of Escherichia coli.
  J Biol Chem, 285, 675-684.  
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.  
20133180 R.E.Silversmith (2010).
Auxiliary phosphatases in two-component signal transduction.
  Curr Opin Microbiol, 13, 177-183.  
20080056 R.Gao, and A.M.Stock (2010).
Molecular strategies for phosphorylation-mediated regulation of response regulator activity.
  Curr Opin Microbiol, 13, 160-167.  
20345663 R.Li, J.Gu, Y.Y.Chen, C.L.Xiao, L.W.Wang, Z.P.Zhang, L.J.Bi, H.P.Wei, X.D.Wang, J.Y.Deng, and X.E.Zhang (2010).
CobB regulates Escherichia coli chemotaxis by deacetylating the response regulator CheY.
  Mol Microbiol, 76, 1162-1174.  
20966074 Z.H.Chen, C.Schilde, and P.Schaap (2010).
Functional dissection of adenylate cyclase R, an inducer of spore encapsulation.
  J Biol Chem, 285, 41724-41731.  
19581368 S.D.Seredick, B.M.Seredick, D.Baker, and G.B.Spiegelman (2009).
An A257V mutation in the bacillus subtilis response regulator Spo0A prevents regulated expression of promoters with low-consensus binding sites.
  J Bacteriol, 191, 5489-5498.  
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.  
19646451 Y.Pazy, A.C.Wollish, S.A.Thomas, P.J.Miller, E.J.Collins, R.B.Bourret, and R.E.Silversmith (2009).
Matching biochemical reaction kinetics to the timescales of life: structural determinants that influence the autodephosphorylation rate of response regulator proteins.
  J Mol Biol, 392, 1205-1220.
PDB codes: 3f7n 3fft 3ffw 3ffx 3fgz
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.  
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.  
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.  
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.  
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
17890312 A.M.del Campo, T.Ballado, J.de la Mora, S.Poggio, L.Camarena, and G.Dreyfus (2007).
Chemotactic control of the two flagellar systems of Rhodobacter sphaeroides is mediated by different sets of CheY and FliM proteins.
  J Bacteriol, 189, 8397-8401.  
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.  
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
16816196 K.Paul, J.G.Harmon, and D.F.Blair (2006).
Mutational analysis of the flagellar rotor protein FliN: identification of surfaces important for flagellar assembly and switching.
  J Bacteriol, 188, 5240-5248.  
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.  
16816192 R.Gao, A.Mukhopadhyay, F.Fang, and D.G.Lynn (2006).
Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens.
  J Bacteriol, 188, 5204-5211.  
17001075 R.Grenha, N.J.Rzechorzek, J.A.Brannigan, R.N.de Jong, E.Ab, T.Diercks, V.Truffault, J.C.Ladds, M.J.Fogg, C.Bongiorni, M.Perego, R.Kaptein, K.S.Wilson, G.E.Folkers, and A.J.Wilkinson (2006).
Structural characterization of Spo0E-like protein-aspartic acid phosphatases that regulate sporulation in bacilli.
  J Biol Chem, 281, 37993-38003.
PDB codes: 2bzb 2c0s
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
16321945 A.Hyakutake, M.Homma, M.J.Austin, M.A.Boin, C.C.Häse, and I.Kawagishi (2005).
Only one of the five CheY homologs in Vibrio cholerae directly switches flagellar rotation.
  J Bacteriol, 187, 8403-8410.  
16321925 D.E.Wemmer, and D.Kern (2005).
Beryllofluoride binding mimics phosphorylation of aspartate in response regulators.
  J Bacteriol, 187, 8229-8230.  
16281059 H.Makyio, R.Iino, C.Ikeda, H.Imamura, M.Tamakoshi, M.Iwata, D.Stock, R.A.Bernal, E.P.Carpenter, M.Yoshida, K.Yokoyama, and S.Iwata (2005).
Structure of a central stalk subunit F of prokaryotic V-type ATPase/synthase from Thermus thermophilus.
  EMBO J, 24, 3974-3983.
PDB code: 2d00
16321923 K.I.Varughese (2005).
Conformational changes of Spo0F along the phosphotransfer pathway.
  J Bacteriol, 187, 8221-8227.  
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
15240481 C.Benda, C.Scheufler, N.Tandeau de Marsac, and W.Gärtner (2004).
Crystal structures of two cyanobacterial response regulators in apo- and phosphorylated form reveal a novel dimerization motif of phytochrome-associated response regulators.
  Biophys J, 87, 476-487.
PDB codes: 1k66 1k68
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.  
15289606 S.Y.Park, B.D.Beel, M.I.Simon, A.M.Bilwes, and B.R.Crane (2004).
In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved.
  Proc Natl Acad Sci U S A, 101, 11646-11651.
PDB code: 1u0s
12511501 G.Alexandre, and I.B.Zhulin (2003).
Different evolutionary constraints on chemotaxis proteins CheW and CheY revealed by heterologous expression studies and protein sequence analysis.
  J Bacteriol, 185, 544-552.  
12614149 J.H.Zhang, G.Xiao, R.P.Gunsalus, and W.L.Hubbell (2003).
Phosphorylation triggers domain separation in the DNA binding response regulator NarL.
  Biochemistry, 42, 2552-2559.  
12591865 R.E.Silversmith, G.P.Guanga, L.Betts, C.Chu, R.Zhao, and R.B.Bourret (2003).
CheZ-mediated dephosphorylation of the Escherichia coli chemotaxis response regulator CheY: role for CheY glutamate 89.
  J Bacteriol, 185, 1495-1502.
PDB code: 1mih
12352955 A.Rinaldo-Matthis, C.Rampazzo, P.Reichard, V.Bianchi, and P.Nordlund (2002).
Crystal structure of a human mitochondrial deoxyribonucleotidase.
  Nat Struct Biol, 9, 779-787.
PDB code: 1mh9
12145642 P.Matsumura (2002).
Last, but not least.
  Nat Struct Biol, 9, 563-564.  
11741839 R.B.Bourret, N.W.Charon, A.M.Stock, and A.H.West (2002).
Bright lights, abundant operons--fluorescence and genomic technologies advance studies of bacterial locomotion and signal transduction: review of the BLAST meeting, Cuernavaca, Mexico, 14 to 19 January 2001.
  J Bacteriol, 184, 1.  
12080332 R.Zhao, E.J.Collins, R.B.Bourret, and R.E.Silversmith (2002).
Structure and catalytic mechanism of the E. coli chemotaxis phosphatase CheZ.
  Nat Struct Biol, 9, 570-575.
PDB code: 1kmi
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.  
12065505 S.Rankin, Z.Li, and R.R.Isberg (2002).
Macrophage-induced genes of Legionella pneumophila: protection from reactive intermediates and solute imbalance during intracellular growth.
  Infect Immun, 70, 3637-3648.  
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
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
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.  
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.