2SKD

PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHATE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE

Replaces:  1SKD

Summary for 2SKD

• Entry DOI: 10.2210/pdb2skd/pdb
• Descriptor: PYRIDOXAL PHOSPHORYLASE B, alpha-D-glucopyranose, PHOSPHATE ION, ... (6 entities in total)
• Functional Keywords: glycogen phosphorylase, glycogen metabolism, allosteric enzyme, pyridoxal phosphate, transferase
• Biological source: Oryctolagus cuniculus (rabbit)
• Total number of polymer chains: 1
• Total formula weight: 98161.68

Authors

Oikonomakos, N.G.,Zographos, S.E.,Tsitsanou, K.E.,Johnson, L.N.,Acharya, K.R. (deposition date: 1998-12-11, release date: 1998-12-16, Last modification date: 2023-08-30)

Primary citation

Oikonomakos, N.G.,Zographos, S.E.,Tsitsanou, K.E.,Johnson, L.N.,Acharya, K.R.
Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal.
Protein Sci., 5:2416-2428, 1996

PubMed Abstract: It has been established that phosphate analogues can activate glycogen phosphorylase reconstituted with pyridoxal in place of the natural cofactor pyridoxal 5'-phosphate (Change YC. McCalmont T, Graves DJ. 1983. Biochemistry 22:4987-4993). Pyridoxal phosphorylase b has been studied by kinetic, ultracentrifugation, and X-ray crystallographic experiments. In solution, the catalytically active species of pyridoxal phosphorylase b adopts a conformation that is more R-state-like than that of native phosphorylase b, but an inactive dimeric species of the enzyme can be stabilized by activator phosphite in combination with the T-state inhibitor glucose. Co-crystals of pyridoxal phosphorylase b complexed with either phosphite, phosphate, or fluorophosphate, the inhibitor glucose, and the weak activator IMP were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the structures of the complexes have been refined to give crystallographic R factors of 18.5-19.2%, for data between 8 and 2.4 A resolution. The anions bind tightly at the catalytic site in a similar but not identical position to that occupied by the cofactor 5'-phosphate group in the native enzyme (phosphorus to phosphorus atoms distance = 1.2 A). The structural results show that the structures of the pyridoxal phosphorylase b-anion-glucose-IMP complexes are overall similar to the glucose complex of native T-state phosphorylase b. Structural comparisons suggest that the bound anions, in the position observed in the crystal, might have a structural role for effective catalysis.

PubMed: 8976550

Experimental method

X-RAY DIFFRACTION (2.4 Å)