Summary for 2PRI
| Entry DOI | 10.2210/pdb2pri/pdb |
| Descriptor | GLYCOGEN PHOSPHORYLASE B, 2-deoxy-6-O-phosphono-alpha-D-glucopyranose, PYRIDOXAL-5'-PHOSPHATE, ... (4 entities in total) |
| Functional Keywords | glycogen phosphorylase, transferase |
| Biological source | Oryctolagus cuniculus (rabbit) |
| Total number of polymer chains | 1 |
| Total formula weight | 97782.48 |
| Authors | Oikonomakos, N.G.,Zographos, S.E.,Johnson, L.N.,Papageorgiou, A.C.,Acharya, K.R. (deposition date: 1998-12-11, release date: 1998-12-14, Last modification date: 2023-08-30) |
| Primary citation | Oikonomakos, N.G.,Zographos, S.E.,Johnson, L.N.,Papageorgiou, A.C.,Acharya, K.R. The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies. J.Mol.Biol., 254:900-917, 1995 Cited by PubMed Abstract: Kinetic and crystallographic studies have characterized the effect of 2-deoxy-glucose 6-phosphate on the catalytic and structural properties of glycogen phosphorylase b. Previous work on the binding of glucose 6-phosphate, a potent physiological inhibitor of the enzyme, to T state phosphorylase b in the crystal showed that the inhibitor binds at the allosteric site and induces substantial conformational changes that affect the subunit-subunit interface. The hydrogen-bond from the O-2 hydroxyl of glucose 6-phosphate to the main-chain oxygen of Val40' represents the only hydrogen bond from the sugar to the other subunit, and this interaction appears important for promoting a more "tensed" structure than native T state phosphorylase b. 2-Deoxy-glucose 6-phosphate acts competitively with both the activator AMP and the substrate glucose 1-phosphate, with Ki values of 0.53 mM and 1.23 mM, respectively. The binding of 2-deoxy-glucose 6-phosphate to T state glycogen phosphorylase b in the crystal, has been investigated and the complex phosphorylase b: 2-deoxy-glucose 6-phosphate has been refined to give a crystallographic R factor of 17.3%, for data between 8 A and 2.3 A. 2-Deoxy-glucose 6-phosphate binds at the allosteric site as the a anomer and adopts a different conformation compared to glucose 6-phosphate. The two conformations differ by 160 degrees in the torsion angle about the C-5-C-6 bond. The contacts from the phosphate group are essentially identical to those made by the phosphate of glucose 6-phosphate but the 2-deoxy glucosyl moiety binds in a quite different orientation compared to the glucosyl of glucose 6-phosphate. 2-Deoxy-glucose 6-phosphate can be accommodated in the allosteric site with very little change in the protein, while structural comparisons show that the phosphorylase b: 2-deoxy-glucose 6-phosphate complex structure is overall more similar to a glucose-like complex than to the Glc-6-P complex structure. PubMed: 7500360DOI: 10.1006/jmbi.1995.0665 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
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