Structural Characterization of Adenine Nucleotides Bound to Escherichia coli Adenylate Kinase. 1. Adenosine Conformations by Proton Two-Dimensional Transferred Nuclear Overhauser Effect Spectroscopy

• Published in: Biochemistry (Easton) 2000-04, Vol.39 (13), p.3636-3646
• Main Authors: Lin, Yan, Nageswara Rao, B. D
• Format: Article
• Language: English
• Subjects: adenine; Adenine Nucleotides - chemistry; adenosine; Adenosine - chemistry; Adenylate Kinase - chemistry; Binding Sites; Escherichia coli; Escherichia coli - enzymology; Guanosine Diphosphate - chemistry; Magnesium - chemistry; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular - methods; Nucleic Acid Conformation; nucleotides; Protons; Titrimetry
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi991921t

Adenosine conformations of adenosine 5‘-triphosphate (ATP) and adenosine 5‘-monophosphate (AMP), and of an ATP analogue, adenylyl imidodiphosphate (AMPPNP), bound to Escherichia coli adenylate kinase (AKe) in the complexes of AKe·Mg(II)ATP, AKe·AMP·Mg(II)GDP, AKe·AMPPNP, and AKe·Mg(II)AMPPNP were determined by transferred two-dimensional nuclear Overhauser effect spectroscopy (TRNOESY) measurements and molecular dynamics simulations. The glycosidic torsion angles, χ, deduced for the adenine nucleotides in these complexes are 51°, 37°, 49°, and 47°, respectively, with an experimental error of about ±5°. These values are in general agreement with those previously measured for other ATP-utilizing enzymes, suggesting a possible common motif for adenosine recognition and binding. The pseudorotational phase angle, P, of the sugar puckers for the bound nucleotides varied between 50° and 103°. These solution-state conformations are significantly different from those in published data from X-ray crystallography. A computation of the ligand NOEs, made by using the program CORCEMA [Moseley, H. N. B., Curto, E. V., and Krishna, N. R. (1995) J. Magn. Reson. B108, 243−261] with the protein protons in the vicinity of nucleotide included, on the basis of the X-ray structure of the AKe·AMP·AMPPNP complex [Berry, M. B., Meador, B., Bilderback, T., Liang, P., Glaser, M., and Philips, G. N., Jr. (1994) Proteins:  Struct., Funct., Genet. 19, 183−198], showed that polarization transfer to the protein protons does not produce significant errors in the structures determined by considering the ligand NOEs alone.