The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP

Proteins. 1994 Jul;19(3):183-98. doi: 10.1002/prot.340190304.


The structure of E. coli adenylate kinase with bound AMP and AMPPNP at 2.0 A resolution is presented. The protein crystallizes in space group C2 with two molecules in the asymmetric unit, and has been refined to an R factor of 20.1% and an Rfree of 31.6%. In the present structure, the protein is in the closed (globular) form with the large flexible lid domain covering the AMPPNP molecule. Within the protein, AMP and AMPPNP, and ATP analog, occupy the AMP and ATP sites respectively, which had been suggested by the most recent crystal structure of E. coli adenylate kinase with Ap5A bound (Müller and Schulz, 1992, ref. 1) and prior fluorescence studies (Liang et al., 1991, ref. 2). The binding of substrates and the positions of the active site residues are compared between the present structure and the E. coli adenylate kinase/Ap5A structure. We failed to detect a peak in the density map corresponding to the Mg2+ ion which is required for catalysis, and its absence has been attributed to the use of ammonium sulfate in the crystallization solution. Finally, a comparison is made between the present structure and the structure of the heavy chain of muscle myosin.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Monophosphate / chemistry*
  • Adenosine Monophosphate / metabolism
  • Adenylate Kinase / chemistry*
  • Adenylate Kinase / metabolism
  • Adenylyl Imidodiphosphate / chemistry*
  • Adenylyl Imidodiphosphate / metabolism
  • Binding Sites
  • Crystallography, X-Ray
  • Dinucleoside Phosphates / chemistry
  • Escherichia coli / enzymology*
  • Hydrogen Bonding
  • Magnesium / chemistry
  • Models, Molecular
  • Motion
  • Protein Conformation
  • Water / chemistry


  • Dinucleoside Phosphates
  • Water
  • Adenylyl Imidodiphosphate
  • Adenosine Monophosphate
  • P(1),P(5)-di(adenosine-5'-)pentaphosphate
  • Adenylate Kinase
  • Magnesium