1p2d: Difference between revisions

Revision as of 15:24, 21 February 2008

Crystal Structure of Glycogen Phosphorylase B in complex with Beta Cyclodextrin

OverviewOverview

A number of regulatory binding sites of glycogen phosphorylase (GP), such as the catalytic, the inhibitor, and the new allosteric sites are currently under investigation as targets for inhibition of hepatic glycogenolysis under high glucose concentrations; in some cases specific inhibitors are under evaluation in human clinical trials for therapeutic intervention in type 2 diabetes. In an attempt to investigate whether the storage site can be exploited as target for modulating hepatic glucose production, alpha-, beta-, and gamma-cyclodextrins were identified as moderate mixed-type competitive inhibitors of GPb (with respect to glycogen) with K(i) values of 47.1, 14.1, and 7.4 mM, respectively. To elucidate the structural basis of inhibition, we determined the structure of GPb complexed with beta- and gamma-cyclodextrins at 1.94 A and 2.3 A resolution, respectively. The structures of the two complexes reveal that the inhibitors can be accommodated in the glycogen storage site of T-state GPb with very little change of the tertiary structure and provide a basis for understanding their potency and subsite specificity. Structural comparisons of the two complexes with GPb in complex with either maltopentaose (G5) or maltoheptaose (G7) show that beta- and gamma-cyclodextrins bind in a mode analogous to the G5 and G7 binding with only some differences imposed by their cyclic conformations. It appears that the binding energy for stabilization of enzyme complexes derives from hydrogen bonding and van der Waals contacts to protein residues. The binding of alpha-cyclodextrin and octakis (2,3,6-tri-O-methyl)-gamma-cyclodextrin was also investigated, but none of them was bound in the crystal; moreover, the latter did not inhibit the phosphorylase reaction.

About this StructureAbout this Structure

1P2D is a Single protein structure of sequence from Oryctolagus cuniculus with as ligand. Active as Phosphorylase, with EC number 2.4.1.1 Full crystallographic information is available from OCA.

ReferenceReference

The binding of beta- and gamma-cyclodextrins to glycogen phosphorylase b: kinetic and crystallographic studies., Pinotsis N, Leonidas DD, Chrysina ED, Oikonomakos NG, Mavridis IM, Protein Sci. 2003 Sep;12(9):1914-24. PMID:12930991

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-[[Image:1p2d.jpg|left|200px]]<br /><applet load="1p2d" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1p2d.jpg|left|200px]]<br /><applet load="1p2d" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1p2d, resolution 1.94&Aring;" />
 '''Crystal Structure of Glycogen Phosphorylase B in complex with Beta Cyclodextrin'''<br />
 ==Overview==
-A number of regulatory binding sites of glycogen phosphorylase (GP), such, as the catalytic, the inhibitor, and the new allosteric sites are, currently under investigation as targets for inhibition of hepatic, glycogenolysis under high glucose concentrations; in some cases specific, inhibitors are under evaluation in human clinical trials for therapeutic, intervention in type 2 diabetes. In an attempt to investigate whether the, storage site can be exploited as target for modulating hepatic glucose, production, alpha-, beta-, and gamma-cyclodextrins were identified as, moderate mixed-type competitive inhibitors of GPb (with respect to, glycogen) with K(i) values of 47.1, 14.1, and 7.4 mM, respectively. To, elucidate the structural basis of inhibition, we determined the structure, of GPb complexed with beta- and gamma-cyclodextrins at 1.94 A and 2.3 A, resolution, respectively. The structures of the two complexes reveal that, the inhibitors can be accommodated in the glycogen storage site of T-state, GPb with very little change of the tertiary structure and provide a basis, for understanding their potency and subsite specificity. Structural, comparisons of the two complexes with GPb in complex with either, maltopentaose (G5) or maltoheptaose (G7) show that beta- and, gamma-cyclodextrins bind in a mode analogous to the G5 and G7 binding with, only some differences imposed by their cyclic conformations. It appears, that the binding energy for stabilization of enzyme complexes derives from, hydrogen bonding and van der Waals contacts to protein residues. The, binding of alpha-cyclodextrin and octakis, (2,3,6-tri-O-methyl)-gamma-cyclodextrin was also investigated, but none of, them was bound in the crystal; moreover, the latter did not inhibit the, phosphorylase reaction.
+A number of regulatory binding sites of glycogen phosphorylase (GP), such as the catalytic, the inhibitor, and the new allosteric sites are currently under investigation as targets for inhibition of hepatic glycogenolysis under high glucose concentrations; in some cases specific inhibitors are under evaluation in human clinical trials for therapeutic intervention in type 2 diabetes. In an attempt to investigate whether the storage site can be exploited as target for modulating hepatic glucose production, alpha-, beta-, and gamma-cyclodextrins were identified as moderate mixed-type competitive inhibitors of GPb (with respect to glycogen) with K(i) values of 47.1, 14.1, and 7.4 mM, respectively. To elucidate the structural basis of inhibition, we determined the structure of GPb complexed with beta- and gamma-cyclodextrins at 1.94 A and 2.3 A resolution, respectively. The structures of the two complexes reveal that the inhibitors can be accommodated in the glycogen storage site of T-state GPb with very little change of the tertiary structure and provide a basis for understanding their potency and subsite specificity. Structural comparisons of the two complexes with GPb in complex with either maltopentaose (G5) or maltoheptaose (G7) show that beta- and gamma-cyclodextrins bind in a mode analogous to the G5 and G7 binding with only some differences imposed by their cyclic conformations. It appears that the binding energy for stabilization of enzyme complexes derives from hydrogen bonding and van der Waals contacts to protein residues. The binding of alpha-cyclodextrin and octakis (2,3,6-tri-O-methyl)-gamma-cyclodextrin was also investigated, but none of them was bound in the crystal; moreover, the latter did not inhibit the phosphorylase reaction.
 ==About this Structure==
-P2D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with PLP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1P2D OCA].
+P2D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P2D OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Phosphorylase]]
 [[Category: Single protein]]
-[[Category: Chrysina, E.D.]]
+[[Category: Chrysina, E D.]]
-[[Category: Leonidas, D.D.]]
+[[Category: Leonidas, D D.]]
-[[Category: Mavridis, I.M.]]
+[[Category: Mavridis, I M.]]
-[[Category: Oikonomakos, N.G.]]
+[[Category: Oikonomakos, N G.]]
 [[Category: Pinotsis, N.]]
 [[Category: PLP]]
 [[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:24:19 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:24:22 2008''