PDBsum entry 1skc

Glycogen phosphorylase

PDB id: 1skc

Contents

Protein chain

831 a.a.

Ligands

GLC

PLP

FPO

IMP

Waters ×562

Obsolete entry

PDB id:

1skc

Name:

Glycogen phosphorylase

Title:

Pyridoxal phosphorylase b in complex with fluorophosphate, glucose and inosine-5'-monophosphate

Structure:

Pyridoxal phosphorylase b. Chain: null. Other_details: in complex with fluorophosphate, glucose and inosine-5'-monophosphate

Source:

Oryctolagus cuniculus. Rabbit. Tissue: muscle

Biol. unit:

Dimer (from PDB file)

Resolution:

2.40Å R-factor: 0.185

Authors:

N.G.Oikonomakos,S.E.Zographos,K.E.Tsitsanou,L.N.Johnson, K.R.Acharya

Key ref:

N.G.Oikonomakos et al. (1996). Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal. Protein Sci, 5, 2416-2428. PubMed id: 8976550 DOI: 10.1002/pro.5560051204

Date:

13-Sep-96 Release date: 11-Jan-97

Protein chain

P00489  (PYGM_RABIT) -  Glycogen phosphorylase, muscle form from Oryctolagus cuniculus

Seq: 843 a.a.

Struc: 831 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.1.1 - glycogen phosphorylase.
• Pathway: Glycogen
• Reaction: [(1->4)-alpha-D-glucosyl](n) + phosphate = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate

[(1->4)-alpha-D-glucosyl](n) + phosphate (Bound ligand (Het Group name = FPO) matches with 6667.00% similarity corresponds exactly) = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate (Bound ligand (Het Group name = IMP) matches with 5000.00% similarity corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/pro.5560051204

Protein Sci 5:2416-2428 (1996)

PubMed id: 8976550

Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal.

N.G.Oikonomakos, S.E.Zographos, K.E.Tsitsanou, L.N.Johnson, K.R.Acharya.

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.