Multiple phosphate positions in the catalytic site of glycogen phosphorylase: Structure of the pyridoxal‐5′‐pyrophosphate coenzyme‐substrate analog

• Published in: Protein science 1992-09, Vol.1 (9), p.1100-1111
• Main Authors: Sprang, Stephen R., Madsen, Neil B., Withers, Stephen G.
• Format: Article
• Language: English
• Subjects: active site; active sites; allosteric control; Amino Acid Sequence; Binding Sites; enzyme mechanism; glycogen; glycogen phosphorylase; Macromolecular Substances; Models, Molecular; phosphorolysis; Phosphorylases - chemistry; Phosphorylases - metabolism; Protein Conformation; Protein Structure, Secondary; pyridoxal diphosphate; pyridoxal monophosphate; pyridoxal phosphate; Pyridoxal Phosphate - metabolism; pyridoxal-5'-diphosphate; R‐state; X-ray crystallography; X-Ray Diffraction
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1002/pro.5560010904

The three‐dimensional structure of an R‐state conformer of glycogen phosphorylase containing the coenzyme‐substrate analog pyridoxal‐5′‐diphosphate at the catalytic site (PLPP‐GPb) has been refined by X‐ray crystallography to a resolution of 2.87 Å. The molecule comprises four subunits of phosphorylase related by approximate 222 symmetry. Whereas the quaternary structure of R‐state PLPP‐GPb is similar to that of phosphorylase crystallized in the presence of ammonium sulfate (Barford, D. & Johnson, L.N., 1989, Nature 340, 609–616), the tertiary structures differ in that the two domains of the PLPP‐GPb subunits are rotated apart by 5° relative to the T‐state conformation. Global differences among the four subunits suggest that the major domains of the phosphorylase subunit are connected by a flexible hinge. The two different positions observed for the terminal phosphate of the PLPP are interpreted as distinct phosphate subsites that may be occupied at different points along the reaction pathway. The structural basis for the unique ability of R‐state dimers to form tetramers results from the orientation of subunits with respect to the dyad axis of the dimer. Residues in opposing dimers are in proper registration to form tetramers only in the R‐state.