1FQW

CRYSTAL STRUCTURE OF ACTIVATED CHEY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of activated CheY. Comparison with other activated receiver domains.

Lee, S.Y.Cho, H.S.Pelton, J.G.Yan, D.Berry, E.A.Wemmer, D.E.

(2001) J.Biol.Chem. 276: 16425-16431

  • DOI: 10.1074/jbc.M101002200
  • Also Cited By: 1ZDM

  • PubMed 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) ...

    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.


    Related Citations: 
    • Phosphorylated Aspartate in the Structure of a Response Regulator Protein
      Lewis, R.J.,Brannigan, J.A.,Muchova, K.,Barak, I.,Wilkinson, A.J.
      (1999) J.Mol.Biol. 294: 9
    • The 1.9A resolution Crystal structure of Phosphono-CheY, an Analogue of the Active Form of the Response Regulator, CheY
      Halkides, C.J.,McEvoy, M.M.,Casper, E.,Matsumura, P.,Volz, K.,Dahlquist, F.W.
      (2000) Biochemistry 39: 5280
    • NMR structure of Activated CheY
      Cho, H.S.,Lee, S.Y.,Yan, D.,Pan, X.,Parkinson, J.S.,Kustu, S.,Wemmer, D.E.,Pelton, J.G.
      (2000) J.Mol.Biol. 297: 543
    • Conformational changes induced by phosphorylation of the FixJ receiver domain
      Birck, C.,Mourey, L.,Gouet, P.,Fabry, B.,Schumacher, J.,Rousseau, P.,Kahn, D.,Samama, J.P.
      (1999) Structure 7: 1505


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHEMOTAXIS CHEY PROTEIN
A, B
128Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: cheY
Find proteins for P0AE67 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AE67
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.684α = 90.00
b = 53.911β = 90.00
c = 161.532γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-24
    Type: Database references