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From Proteopedia

Introduction and General Structure

can be observed. Aldolase is an enzyme that is active during glycolysis, which is an overall series of reactions that produces cellular energy (ATP). Specifically, aldolase catalyzes an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and glycerone phosphate. Aldolase is a tetrameter (four subunits)composed of alpha helices and beta sheets (). Please note that alpha helices are observed in blue, and beta sheets are in yellow. The majority of the helices are located on the surface (outside) of the enzyme, where as most of the sheets are found in the interior (inside). Most likely, polar amino acids are located on the peripheral helices, while hydrophobic or paired-polar amino acids are found within the beta sheets.

Hydrogen and Disulfide Bonds

The for aldolase allow the protein proper stability. Hydrogen bonds are in red (there are plenty of them), and disfulfide bonds would appear as black. However, please note that there are no observable disulfide bonds in this picture. Also, after observing the hydrogen bonds, the beta sheets can be identified as parallel because the hydrogen bonds appear as slanted (or strained) between sheets, which indicates that specific type of interaction.

Hydrophobic and Hydrophilic Residues

The are observed in grey. These residues are mostly observed in the interior of the enzyme (possibly on the beta sheets). Thus, they are hidden from the aqueous solvent. The are observed in red. Notice that the majority of the hydrophilic amino acids are located on the alpha helices that are on the outside of this enzyme. Thus, these residues must interact with the solvent, which is aqueous. Plus, notice that there are about equal amounts of hydrophobic and hydrophilic residues.

Solvent

The that surround the enzyme are observed in blue. The water appears only on the outside of the enzyme. Thus, the interior must contain hydrophobic residues, and water excludes these from solvation (because when water interacts with hydrophobic residues, there is a decrease in entropy - thus, water tries to minimize contact with these amino acids). The exterior of the protein must contain hydrophilic residues that will interact with the water molecules, as all of the blue water molecules surround the exterior of the enzyme.

The Ligands and Ligand Contacts

The for chain A is observed in blue. The actual substrate (1,3-dihydroxyacetonephosphate [C3H7O6P], which is a glyceraldehyde 3-phosphate analog) is in red. The rest of the enzyme is colored in yellow. There should be 3 other ligand binding sites (what is observed in blue) in chains B, C, and D (not shown). Zinc (also not shown in the structure) is an cofactor that helps drive the aldol reaction catalyzed by aldolase. Please note that this cofactor is used mainly for catalysis and does not significantly add to the structure of the enzyme. The are Ser271, Gly272, Gly302, Lys229, Arg303, Lys146, and Asn33 (binding residues are in red, the substrate is in mint, and the entire binding site is in blue). These residues (red) interact with and stabilize the substrate (mint) within the active site.

Catalytic Residues

The are displayed in red. They are Asn33, Glu187, and Lys229, all of which help catalyze an aldol cleavage reaction that hydrolyzes fructose 1,6-bisphosphate into glycerone phosphate and glyceraldehyde 3-phosphate. The lysine residue plays a major role in the molecule's catalysis. The positive charge present on the side chain's nitrogen atom attacks the substrate to begin aldol catalysis. Again, each other chain (B, C, and D) would have their own set of these residues (not shown).

References

1. M.St-Jean et al. (2009). Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase. Biochemistry, 48, 4528-4537. PubMed id: 19354220 DOI: 10.1021/bi8021558

2. http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

3. http://www.rcsb.org/pdb/explore/explore.do?structureId=3DFO