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 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1FQW

  • 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) and Lys(109), respectively ...

    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: 
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHEMOTAXIS CHEY PROTEINA, B128Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AE67 (Escherichia coli (strain K12))
Explore P0AE67 
Go to UniProtKB:  P0AE67
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEF
Query on BEF

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 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 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.684α = 90
b = 53.911β = 90
c = 161.532γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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