Sandbox Reserved 795

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This Sandbox is Reserved from Oct 10, 2013, through May 20, 2014 for use in the course "CHEM 410 Biochemistry 1 and 2" taught by Hanna Tims at the Messiah College. This reservation includes Sandbox Reserved 780 through Sandbox Reserved 807.
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Contents

Introduction and General Structure

Glyceraldehyde-3-phosphate dehydrogenase

Drag the structure with the mouse to rotate

, or G-3-P dehydrogenase, is an enzyme that plays a significant role in metabolism. It catalyzes a step in glycolysis in which glyceraldehyde 3-phosphate is converted to 3-phospho-D-glyceroyl phosphate with the help of NAD. This particular enzyme is human placental G-3-P dehydrogenase. It is a tetramer protein made up of four subunits. The of G-3-P dehydrogenase consists of alpha helices which are displayed in yellow and beta sheets which are displayed in pink. The majority of the beta sheets are parallel, however there are some antiparallel sheets as well. It seems as though the majority of the alpha helices are located around the outside of the enzyme, suggesting that they are made up of polar or charged amino acids that will interact with the aqueous environment.

Hydrogen Bonds

The of the backbone is displayed in black. Hydrogen bonding helps to stabilize the structure. Where the beta sheets are parallel, the hydrogen bonds are slanted. Where the beta sheets are antiparallel, the hydrogen bonds are straight. There are no disulfide bonds present in this enzyme.

Hydrophilic and Hydrophobic Residues

The are displayed in gray. They are buried in the interior of the molecule so they can be shielded from the aqueous environment. The are displayed in red. They occupy the outer portions of the molecule. These residues are polar or charged and therefore readily interact with the aqueous environment.

Solvent Accessibility

In an aqueous environment, water is a solvent that surrounds and interacts with many enzymes and molecules. are displayed as the yellow spheres and it can be seen that they are located along the outside surface of the enzyme where the hydrophilic amino acid residues are located. The interior of the molecule does not contain very many water molecules, because this is where the hydrophobic residues are located and their interaction with water is not energetically favored.

Cofactor and Cofactor Binding Sites

For this enzyme, NAD is the cofactor involved in the reaction. The for this enzyme are displayed in green. Note that only three of the subunits of this protein contain NAD binding sites and each of them bind an NAD molecule. The amino acids that are specifically involved in binding include isoleucine, aspartic acid, asparagine, and arginine. The majority of these residues are polar which makes sense seeing that they are binding to a polar molecule.

A zoomed in image of the is shown here. The NAD molecule is depicted as gray, blue, and red, and it is the molecule in the center that is bound to the NAD binding site. The polar residues surrounding the NAD help to facilitate binding.

Catalytic Residues

The for each subunit are displayed in black. They include His179 and Cys152. These residues are located in the active site and help catalyze the binding of NAD to the ligand binding site. A zoomed in image of the is shown here.

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