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Volume 11, Issue 9, Pages 1071-1085 (September 2003)
X-Ray Crystallographic and Kinetic Studies of Human Sorbitol Dehydrogenase Thomas A. Pauly, Jennifer L. Ekstrom, David A. Beebe, Boris Chrunyk, David Cunningham, Matthew Griffor, Ajith Kamath, S.Edward Lee, Rebecca Madura, Dewitt Mcguire, Timothy Subashi, David Wasilko, Paul Watts, Banavara L. Mylari, Peter J. Oates, Paul D. Adams, Virginia L. Rath Structure Volume 11, Issue 9, Pages (September 2003) DOI: /S (03)
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Figure 1 Substrates, Cofactors, and Inhibitors of hSDH
(A) The polyol pathway consists of two enzymes: aldose reductase (AR) and sorbitol dehydrogenase (SDH). The structures of sorbitol and fructose are shown with their respective carbon atoms numbered. The nicotinamide ring of NAD+ and NADH are shown, R represents the adenine dinucleotide portion of both molecules (omitted for simplicity). (B) Prodrug SDI-157 and CP-166,572 (= SDI-158 [7], WAY [32]). Structures and inhibition constants (IC50) for each molecule are shown. Figures made in ChemDraw (CambridgeSoft, 2001). Structure , DOI: ( /S (03) )
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Figure 2 Overall View of hSDH
(A) Biological tetramer of human sorbitol dehydrogenase. A ribbon diagram of the tetramer coordinates derived from complex of hSDH with zinc, NADH, and CP-166,572, which are shown as stick figures. Subunit A is colored green, B is blue, C is yellow, and D is red. All figures prepared using Ribbons (Carson, 1991) with atoms colored as follows: zinc, purple; carbon, green; nitrogen, blue; oxygen, red; sulfur, yellow; and water molecules, red spheres. (B) Structure of the monomer of human sorbitol dehydrogenase. Ribbon diagram showing the overall fold of one subunit of human sorbitol dehydrogenase and the location of CP-166,572, NADH, and the catalytic zinc atom. Structure , DOI: ( /S (03) )
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Figure 3 Functional and Structural Consequences of Ligand Binding to hSDH (A) Stoichiometry and codependence of ligand binding to hSDH. n = 3, details as described in Experimental Procedures. (B) Zn ligands in hSDH (native). Stereo image showing residues coordinating the catalytic zinc (dashed lines) in hSDH in the absence of NAD(H) or other ligands. (C) Changes in hSDH on binding NAD+. Stereoview of superposition of Cα carbons of hSDH native (gray) and hSDH complexed with NAD+ (green). Electron density for NAD+ is derived from a Fo − Fc omit map contoured at 1σ above the mean. Residues whose side or main chain atoms differ between the two coordinate sets are shown. Structure , DOI: ( /S (03) )
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Figure 4 Inhibition of hSDH by CP-166,572
Experimental details as described in Experimental Procedures. (A) Uncompetitive inhibition of hSDH by CP-166,572 with respect to NAD+. Forward direction, human SDH. (B) Uncompetitive inhibition of hSDH by CP-166,572 with respect to sorbitol. Forward direction, human SDH. (C) Uncompetitive inhibition of hSDH by CP-166,572 with respect to NADH. Reverse direction, human SDH. (D) Competitive inhibition of hSDH by CP-166,572 with respect to fructose. Reverse direction, human SDH (500 μM NADH). (E) Mixed noncompetitive inhibition of hSDH by CP-166,572 with respect to fructose. Reverse direction, human SDH (50 μM NADH). (F) Competitive inhibition of hSDH by CP-166,572 with respect to fructose for sheep SDH. Reverse direction, sheep SDH (500 μM NADH). Structure , DOI: ( /S (03) )
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Figure 5 Binding Site of Inhibitor CP-166,572
(A) Electron density for the inhibitor. Derived from a 2Fo − Fc omit map contoured at 1σ above the mean. (B) CP-166,572 interacts with both Zn and NADH. Stereo image showing the simultaneous interaction between the inhibitor and the catalytic zinc as well as the nicotinamide ring of NADH. All other ligands to zinc are shown. (C) Binding site of CP-166,572. Stereo image showing importance of hydrophobic contacts in binding inhibitor. All residues (gray carbon atoms) within van der Waals distance to CP-166,572 (green carbon atoms) are shown. Only a single direct hydrogen bond is formed to the enzyme (to Glu155); all other hydrogen bonds are formed to water molecules (red spheres). Structure , DOI: ( /S (03) )
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Figure 6 Model of Fructose Binding and Catalyic Mechanism
(A) Stereo image of proposed binding site for fructose (green carbon atoms) superimposed on bound CP-166,572 (in light gray). In this position, the C1 and C2 oxygens of fructose are directly coordinated to zinc, and the C2 carbon is correctly aligned with the C4 atom of NADH, poised for the reverse reaction. (B) Model for reduction of sorbitol to fructose, followed by cyclization of fructose. (1) A schematic of the zinc ligands derived from the native crystal structure. (2) Sorbitol binds after NAD+, resulting in the zinc atom being penta-coordinated; the arrows depict the electron movement entailed in oxidation of the C2 carbon to form fructose with hydride transfer to NAD+. (3) Reverse flow of electrons from NADH to reduce fructose to sorbitol. (3A) Cyclization to the furanose form of fructose. (4) Release of product with zinc coordination returning to the tetra-coordinated state. Structure , DOI: ( /S (03) )
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