Analysis of the surface topography of glycogen phosphorylase a: implications for metabolic interconversion and regulatory mechanisms

Computer drawings of the van der Waals contours of atoms on the surface represent the phosphorylase molecule at 2.5 Å (1 Å = 0.1 nm) resolution with color coding for acidic and basic residues, bound ligands, or conformational changes. The asymmetry resulting from the twofold axis of each dimer provides two faces which can be distinguished structurally and functionally. Thus, a concave catalytic face contains the glycogen storage sites on its periphery with entrances to the glucose-1-phosphate binding sites of the active centers, adjacent to the pyridoxal phosphate moieties, near its center. Just outside the active site is a binding site for negative effectors such as caffeine. On the side of the dimer opposite to the catalytic face is found a convex control face containing the binding sites for the allosteric activator AMP, for which ATP also competes. Quite close to these sites are found the Ser-14-phosphates hydrogen bonded to Arg-69 and Arg-43′ of the symmetry-related monomer. Each Ser-14-phosphate is surrounded by positive charges, including more than are found on adjacent sequences, and therefore, comparative studies on peptides cannot describe fully the specificity and binding requirements of the kinase and phosphatase.The surface topography of the glucose stabilized T state (taut) and the changes which occur during the allosteric transitions induced by AMP and substrates are discussed in terms of their functional implications for the control of both the intrinsic enzymic activity and of the metabolic interconversions between the a and b forms. In particular, the two conformational states (taut and relaxed) exhibit different structural arrangements of the binding sites for the negative effector, caffeine, and the positive effector, AMP. Linkage between the various effector sites is demonstrated by conformational changes in the surface topography. Since the control face is opposite to the catalytic face, the interconverting enzymes can bind to, and act on, the phosphorylase while the latter is bound to glycogen. The Ser-14 residues are only 40 Å apart across the control face and could be bridged readily by the multimeric kinase (α4β4γ4δ4, 1 300 000 daltons) or the large molecular weight form of the phosphatase. The T →R conformational change causes the Ser-14-phosphate to move 5 Å in from the surface, which may be related to the 20-fold decrease of the phosphatase Vm with unchanged Km.