PDBsum entry 1fty

Transferase

PDB id: 1fty

Contents

Protein chain

830 a.a. *

Ligands

GL7

PLP

Waters ×223

* Residue conservation analysis

PDB id:

1fty

Name:

Transferase

Title:

Structures of glycogen phosphorylase-inhibitor complexes and the implications for structure-based drug design

Structure:

Glycogen phosphorylase. Chain: a. Ec: 2.4.1.1

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Tissue: muscle

Biol. unit:

Dimer (from PDB file)

Resolution:

2.38Å R-factor: 0.194 R-free: 0.243

Authors:

K.A.Watson,K.E.Tsitsanou,M.Gregoriou,S.E.Zographos,V.T.Skamnaki, N.G.Oikonomakos,G.W.Fleet,L.N.Johnson

Key ref:

K.A.Watson et al. (2005). Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase. Proteins, 61, 966-983. PubMed id: 16222658 DOI: 10.1002/prot.20653

Date:

13-Sep-00 Release date: 04-Oct-00

Protein chain

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

Seq: 843 a.a.

Struc: 830 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 = [(1->4)-alpha-D-glucosyl](n-1) + alpha-D-glucose 1-phosphate (Bound ligand (Het Group name = PLP) matches with 63.16% similarity)

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

Added reference

DOI no: 10.1002/prot.20653

Proteins 61:966-983 (2005)

PubMed id: 16222658

Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase.

K.A.Watson, E.D.Chrysina, K.E.Tsitsanou, S.E.Zographos, G.Archontis, G.W.Fleet, N.G.Oikonomakos.

ABSTRACT

Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and N-acetyl-beta-D-glucopyranosylamine have been identified as the most potent inhibitors of GP that bind at the catalytic site. Four spirohydantoin and three beta-D-glucopyranosylamine analogs have been designed, synthesized and tested for inhibition of GP in kinetic experiments. Depending on the functional group introduced, the K(i) values varied from 16.5 microM to 1200 microM. In order to rationalize the kinetic results, we determined the crystal structures of the analogs in complex with GP. All the inhibitors bound at the catalytic site of the enzyme, by making direct and water-mediated hydrogen bonds with the protein and by inducing minor movements of the side chains of Asp283 and Asn284, of the 280s loop that blocks access of the substrate glycogen to the catalytic site, and changes in the water structure in the vicinity of the site. The differences observed in the Ki values of the analogs can be interpreted in terms of variations in hydrogen bonding and van der Waals interactions, desolvation effects, ligand conformational entropy, and displacement of water molecules on ligand binding to the catalytic site.

Selected figure(s)

Figure 1.
Figure 1. A schematic diagram of the GPb dimeric molecule viewed down the molecular dyad. One subunit is colored in dark green and the other in light green. The position is shown for the catalytic site. The catalytic site, marked by glucose (GLC) and the essential cofactor pyridoxal 5 -phosphate (PLP), shown in ball-and-stick representations, is buried at the center of the subunit and is accessible to the bulk solvent through a 15-Å long channel. Close-up: Details of the interactions of glucose with residues of the catalytic site. -D-Glucose, a competitive inhibitor (K[i] = 1.7 mM), on binding at the catalytic site, promotes the less active T state through stabilization of the closed position of the 280s loop (shown in cream) which blocks access for the substrate (glycogen) to the catalytic site. In particular, the -1-OH is hydrogen-bonded to Asp283 (OD1), through a water molecule, and the 2-OH is hydrogen-bonded directly to Asn284 (ND2).

Figure 2.
Figure 2. Interactions of compound 1 (A), compound 2 (B), compound 3 (C), compound 4 (D), compound 5 (E), compound 6 (F), compound 7 (G), compound 8 (H), compound 8, 100 K (I), compound 9 (J), compound 10 (K) with GPb in the vicinity of the catalytic site, shown in stereo. The interactions of the glucopyranose ring are retained throughout the structures analyzed and were not incorporated in the figures for clarity reasons.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 966-983) copyright 2005.

Author's comment

Βased on the knowledge derived from former systematic kinetic and crystallographic studies of structurally similar compounds such as alpha-anhydro-glucoheptonic acids and N-acyl derivatives of beta-D-glucopyranosylamine, of which alpha-D-glucoheptonamide (Ki = 0.37 mM) and N-acetyl-beta-D-glucopyranosylamine (Ki = 0.032 mM) were exceptional, and one heterocyclic compound, the spirohydantoin of glucopyranose (Ki = 0.003 mM), which is 550-times better inhibitor than alpha-D-glucose. Starting with these core structures, eight new compounds were designed, synthesized, and studied by kinetic and X-ray crystallographic methods. As predicted, these analogues bound at the catalytic site of GP. The analyses of the molecular interactions of the bound GP-ligand complexes provide a rationale for the different kinetic properties of the inhibitors (see also Archontis et al. (2005) Proteins 61, 984-998. PubMed: 16245298).