Structure of Triphosphoryl Nucleotide Bound at the Active Site of Yeast Hexokinase: ¹H-Nuclear Magnetic Resonance Study

Abstract

Conformation of a nonhydrolyzable adenosine triphosphate (ATP) analogue, adenylyl-(β,γ-methylene)-diphosphonate (AMPPCP) bound at the active site of yeast hexokinase-PII was determined by proton two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY) and molecular dynamics simulations. The effect of the glucose-induced domain closure on the conformation of the nucleotide was evaluated by making measurements on two different complexes: PII•AMPPCPMg(II) and PII•Glc•AMPPCPMg(II). TRNOE measurements were made at 500 MHz, 10°C, as a function of several mixing times varying in the range of 40 to 200 ms. Interproton distances derived from the analysis of NOE buildup curves were used as restraints in molecular dynamics simulations to determine the conformation of the enzyme bound nucleotide. The adenosine moiety was found to bind in high anti conformation with a glycosidic torsion angle χ = 48 ± 5 degrees in both complexes. However, significant differences in the conformations of the ribose and triphosphoryl chain of the nucleotide are observed between the two complexes. The phase angles of pseudorotation P in PII•AMPPCPMg(II) and PII•Glc•AMPPCPMg(II) are 87 degrees and 77 degrees, describing a OE and OT₄ sugar pucker and the amplitudes of the sugar pucker (τ) are 37 degrees and 61 degrees, respectively.