Nucleotide Binding to Pig Muscle 3-Phosphoglycerate Kinase in the Crystal and in Solution:  Relationship between Substrate Antagonism and Interdomain Communication

Binding constants for the nucleotide substrates were determined in two different crystalline forms of pig muscle 3-phosphoglycerate kinase (PGK): the binary complex with 3-phosphoglycerate (3-PG) in which the two domains are in an open conformation (Harlos, Vas, and Blake (1992) Proteins, 12, 133−144) and the ternary complex with 3-PG and the Mg salt of the ATP analogue, β,γ-methyleneadenosine-5‘-triphosphate (AMP-PCP), the structure of which is under resolution. Competitive titrations have been performed in the presence of the chromophoric analogue of ATP, 2‘3‘-O-(2,4,6-trinitrophenyl)ATP (TNP-ATP), similar to those previously carried out in solution, where a weakening of the binding of the nucleotide substrates in the presence of the other substrate, 3-PG, has been observed (Vas, Merli, and Rossi (1994) Biochem. J. 301, 885−891). Here the K d values for MgADP were found to be 0.096 ± 0.021 and 0.045 ± 0.016 mM, respectively, for the crystals of the binary and ternary complexes. Both K d values are significantly smaller than the one obtained in solution in the presence of 3-PG (0.38 ± 0.05 mM) and are close to the values determined in solution in the absence of 3-PG (0.06 ± 0.01 mM). Thus, the “substrate antagonism” observed in solution is not present in either of the investigated crystal forms. Further nucleotide binding studies with the solubilized enzyme have shown that 3-PG has no effect on ADP (Mg2+-free) binding (K d = 0.34 ± 0.05 mM), while it weakens MgADP binding. Thus, 3-PG abolishes the strengthening effect of the Mg2+ ion on the binding of ADP. This phenomenon is apparently due to the interaction between the carboxyl group of 3-PG and the protein, since the carboxyl-lacking analogue glycerol-3-phosphate has no detectable effect on MgADP binding. Comparison of the crystallographic data of different PGK binary (with either 3-PG or MgADP) and ternary (with both 3-PG and MgADP) complexes, having open and closed conformations, respectively, provides a possible structural explanation of the substrate antagonism. We suggest that the specific interaction between the 3-PG carboxylic group and a conserved arginine side chain is changed during domain closure, and, through interdomain communication, this change may be transmitted to the site in which Mg2+ binds the ADP phosphates. This effect is abolished in the crystals of pig muscle PGK, in which lattice forces stabilize the open domain conformation.