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PDBsum entry 1fqw

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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
1fqw
Jmol
Contents
Protein chains
128 a.a. *
Ligands
BEF ×2
Metals
_MN ×2
Waters ×173
* Residue conservation analysis
PDB id:
1fqw
Name: Signaling protein
Title: Crystal structure of activated chey
Structure: Chemotaxis chey protein. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.37Å     R-factor:   0.210     R-free:   0.240
Authors: S.Y.Lee,H.S.Cho,J.G.Pelton,D.Yan,E.A.Berry,D.E.Wemmer
Key ref:
S.Y.Lee et al. (2001). Crystal structure of activated CheY. Comparison with other activated receiver domains. J Biol Chem, 276, 16425-16431. PubMed id: 11279165 DOI: 10.1074/jbc.M101002200
Date:
07-Sep-00     Release date:   18-Jul-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.
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: 10.1074/jbc.M101002200 J Biol Chem 276:16425-16431 (2001)
PubMed id: 11279165  
 
 
Crystal structure of activated CheY. Comparison with other activated receiver domains.
S.Y.Lee, H.S.Cho, J.G.Pelton, D.Yan, E.A.Berry, D.E.Wemmer.
 
  ABSTRACT  
 
The crystal structure of BeF(3)(-)-activated CheY, with manganese in the magnesium binding site, was determined at 2.4-A resolution. BeF(3)(-) bonds to Asp(57), the normal site of phosphorylation, forming a hydrogen bond and salt bridge with Thr(87) and Lys(109), respectively. The six coordination sites for manganese are satisfied by a fluorine of BeF(3)(-), the side chain oxygens of Asp(13) and Asp(57), the carbonyl oxygen of Asn(59), and two water molecules. All of the active site interactions seen for BeF(3)(-)-CheY are also observed in P-Spo0A(r). Thus, BeF(3)(-) activates CheY as well as other receiver domains by mimicking both the tetrahedral geometry and electrostatic potential of a phosphoryl group. The aromatic ring of Tyr(106) is found buried within a hydrophobic pocket formed by beta-strand beta4 and helix H4. The tyrosine side chain is stabilized in this conformation by a hydrogen bond between the hydroxyl group and the backbone carbonyl oxygen of Glu(89). This hydrogen bond appears to stabilize the active conformation of the beta4/H4 loop. Comparison of the backbone coordinates for the active and inactive states of CheY reveals that only modest changes occur upon activation, except in the loops, with the largest changes occurring in the beta4/H4 loop. This region is known to be conformationally flexible in inactive CheY and is part of the surface used by activated CheY for binding its target, FliM. The pattern of activation-induced backbone coordinate changes is similar to that seen in FixJ(r). A common feature in the active sites of BeF(3)(-)-CheY, P-Spo0A(r), P-FixJ(r), and phosphono-CheY is a salt bridge between Lys(109) Nzeta and the phosphate or its equivalent, beryllofluoride. This suggests that, in addition to the concerted movements of Thr(87) and Tyr(106) (Thr-Tyr coupling), formation of the Lys(109)-PO(3)(-) salt bridge is directly involved in the activation of receiver domains generally.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Ribbon diagram of the two BeF[ - ]-activated CheY molecules in the asymmetric unit. The active sites are directed toward the reader. Side chains are shown for BeF[ - ]-Asp57, Thr87, and Tyr106.
Figure 3.
Fig. 3. Stereo view of the active site of BeF[ - ]-CheY. Carbon, nitrogen, oxygen beryllofluoride, and manganese atoms are colored gray, dark blue, red, yellow, and green, respectively. a, omit map contoured at 3.0 covering Asp12, Asp13, BeF[ - ]-Asp57, Thr87, Lys109, and two water molecules. This map was calculated with the occupancies for these residues set to zero. For clarity, the density for manganese is not shown. b, ball-and-stick diagram of the BeF[ - ]-activated CheY active site. Dashed lines and numbers denote active site interactions defined in Table II. c, stereo view of active site residues for BeF[ - ]-CheY(Mn2+) (blue), phosphorylated FixJr(no metal) (lime), and phosphorylated Spo0A^r(Ca^2+) (copper). Mn2+ and Ca^2+ are shown as red and green balls, respectively. Residue numbers are based on E. coli CheY. For clarity, phosphono-CheY was not included.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 16425-16431) copyright 2001.  
  Figures were selected by the author.  

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
20192973 N.R.Williamson, P.M.Commander, and G.P.Salmond (2010).
Quorum sensing-controlled Evr regulates a conserved cryptic pigment biosynthetic cluster and a novel phenomycin-like locus in the plant pathogen, Pectobacterium carotovorum.
  Environ Microbiol, 12, 1811-1827.  
20211578 R.B.Bourret (2010).
Receiver domain structure and function in response regulator proteins.
  Curr Opin Microbiol, 13, 142-149.  
19218445 A.Francez-Charlot, J.Frunzke, C.Reichen, J.Z.Ebneter, B.Gourion, and J.A.Vorholt (2009).
Sigma factor mimicry involved in regulation of general stress response.
  Proc Natl Acad Sci U S A, 106, 3467-3472.  
19714199 B.A.Kidd, D.Baker, and W.E.Thomas (2009).
Computation of conformational coupling in allosteric proteins.
  PLoS Comput Biol, 5, e1000484.  
19411326 J.M.Eraso, and S.Kaplan (2009).
Half-Site DNA sequence and spacing length contributions to PrrA binding to PrrA site 2 of RSP3361 in Rhodobacter sphaeroides 2.4.1.
  J Bacteriol, 191, 4353-4364.  
19800110 P.Casino, V.Rubio, and A.Marina (2009).
Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction.
  Cell, 139, 325-336.
PDB codes: 3dge 3dgf 3gl9
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.  
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
18832306 D.Ruiz, P.Salinas, M.L.Lopez-Redondo, M.L.Cayuela, A.Marina, and A.Contreras (2008).
Phosphorylation-independent activation of the atypical response regulator NblR.
  Microbiology, 154, 3002-3015.  
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
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
18560010 Q.Cui, and M.Karplus (2008).
Allostery and cooperativity revisited.
  Protein Sci, 17, 1295-1307.  
18557815 S.A.Thomas, J.A.Brewster, and R.B.Bourret (2008).
Two variable active site residues modulate response regulator phosphoryl group stability.
  Mol Microbiol, 69, 453-465.  
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
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
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.  
17697997 P.Wassmann, C.Chan, R.Paul, A.Beck, H.Heerklotz, U.Jenal, and T.Schirmer (2007).
Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition.
  Structure, 15, 915-927.
PDB code: 2v0n
17182055 R.Arribas-Bosacoma, S.K.Kim, C.Ferrer-Orta, A.G.Blanco, P.J.Pereira, F.X.Gomis-Rüth, B.L.Wanner, M.Coll, and M.Solà (2007).
The X-ray crystal structures of two constitutively active mutants of the Escherichia coli PhoB receiver domain give insights into activation.
  J Mol Biol, 366, 626-641.
PDB codes: 2jb9 2jba
17050920 A.M.Stock, and J.Guhaniyogi (2006).
A new perspective on response regulator activation.
  J Bacteriol, 188, 7328-7330.  
16784239 C.Laguri, R.A.Stenzel, T.J.Donohue, M.K.Phillips-Jones, and M.P.Williamson (2006).
Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides.
  Biochemistry, 45, 7872-7881.  
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.  
16740923 M.Y.Galperin (2006).
Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
  J Bacteriol, 188, 4169-4182.  
16624907 P.Goymer, S.G.Kahn, J.G.Malone, S.M.Gehrig, A.J.Spiers, and P.B.Rainey (2006).
Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype.
  Genetics, 173, 515-526.  
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.  
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
17038117 V.Menon, D.Li, N.Chauhan, R.Rajnarayanan, A.Dubrovska, A.H.West, and R.Calderone (2006).
Functional studies of the Ssk1p response regulator protein of Candida albicans as determined by phenotypic analysis of receiver domain point mutants.
  Mol Microbiol, 62, 997.  
16321925 D.E.Wemmer, and D.Kern (2005).
Beryllofluoride binding mimics phosphorylation of aspartate in response regulators.
  J Bacteriol, 187, 8229-8230.  
16321923 K.I.Varughese (2005).
Conformational changes of Spo0F along the phosphotransfer pathway.
  J Bacteriol, 187, 8221-8227.  
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.  
16154086 M.Milani, L.Leoni, G.Rampioni, E.Zennaro, P.Ascenzi, and M.Bolognesi (2005).
An active-like structure in the unphosphorylated StyR response regulator suggests a phosphorylation- dependent allosteric activation mechanism.
  Structure, 13, 1289-1297.
PDB codes: 1yio 1zn2
16154092 P.Bachhawat, G.V.Swapna, G.T.Montelione, and A.M.Stock (2005).
Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states.
  Structure, 13, 1353-1363.
PDB code: 1zes
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
15569936 C.Chan, R.Paul, D.Samoray, N.C.Amiot, B.Giese, U.Jenal, and T.Schirmer (2004).
Structural basis of activity and allosteric control of diguanylate cyclase.
  Proc Natl Acad Sci U S A, 101, 17084-17089.
PDB code: 1w25
15090529 C.J.Bent, N.W.Isaacs, T.J.Mitchell, and A.Riboldi-Tunnicliffe (2004).
Crystal structure of the response regulator 02 receiver domain, the essential YycF two-component system of Streptococcus pneumoniae in both complexed and native states.
  J Bacteriol, 186, 2872-2879.
PDB codes: 1nxo 1nxp 1nxt 1nxw
15039551 D.Mukhopadhyay, U.Sen, J.Zapf, and K.I.Varughese (2004).
Metals in the sporulation phosphorelay: manganese binding by the response regulator Spo0F.
  Acta Crystallogr D Biol Crystallogr, 60, 638-645.
PDB code: 1pey
15573139 G.H.Wadhams, and J.P.Armitage (2004).
Making sense of it all: bacterial chemotaxis.
  Nat Rev Mol Cell Biol, 5, 1024-1037.  
14731287 J.G.Smith, J.A.Latiolais, G.P.Guanga, J.D.Pennington, R.E.Silversmith, and R.B.Bourret (2004).
A search for amino acid substitutions that universally activate response regulators.
  Mol Microbiol, 51, 887-901.  
12598367 D.L.Stokes, and N.M.Green (2003).
Structure and function of the calcium pump.
  Annu Rev Biophys Biomol Struct, 32, 445-468.  
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.  
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
12486063 Y.Chen, C.Birck, J.P.Samama, and F.M.Hulett (2003).
Residue R113 is essential for PhoP dimerization and function: a residue buried in the asymmetric PhoP dimer interface determined in the PhoPN three-dimensional crystal structure.
  J Bacteriol, 185, 262-273.  
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
11966823 D.Devos, J.Garmendia, V.de Lorenzo, and A.Valencia (2002).
Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: a structural model of its N-terminal domain.
  Environ Microbiol, 4, 29-41.  
12022879 G.S.Anand, and A.M.Stock (2002).
Kinetic basis for the stimulatory effect of phosphorylation on the methylesterase activity of CheB.
  Biochemistry, 41, 6752-6760.  
  12372152 P.M.Wolanin, P.A.Thomason, and J.B.Stock (2002).
Histidine protein kinases: key signal transducers outside the animal kingdom.
  Genome Biol, 3, REVIEWS3013.  
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.  
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
12081483 S.D.Lahiri, G.Zhang, D.Dunaway-Mariano, and K.N.Allen (2002).
Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis.
  Biochemistry, 41, 8351-8359.
PDB code: 1lvh
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.  
12206664 S.Park, H.Zhang, A.D.Jones, and B.T.Nixon (2002).
Biochemical evidence for multiple dimeric states of the Sinorhizobium meliloti DctD receiver domain.
  Biochemistry, 41, 10934-10941.  
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
11459948 P.R.Thompson, and P.A.Cole (2001).
Probing the mechanism of enzymatic phosphoryl transfer with a chemical trick.
  Proc Natl Acad Sci U S A, 98, 8170-8171.  
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.