Sandbox 38

From Proteopedia

is an enzyme that catalyzes the reaction ATP + AMP = 2ADP. It consists of two identical subunits, A (shown in blue) and B (shown in green). For simplicity's sake, only the A chain will be shown in subsequent green links.

Basic structural elements

Like many proteins, the of adenylate kinase consists of two elements: alpha-helices, which are shown in light green, and beta-sheets, which are shown in dark green. Some of these are parallel, while others are anti-parallel. (Non-repetitive structural elements are shown in light blue/gray.) In addition to the regular hydrogen bonding that results in the secondary structure of the protein, additional is present in the backbone of adenylate kinase (shown in yellow), which also contributes to the overall stability/folding of the molecule. An additional, significant factor in the structural stability/folding of the molecule is the polarity of the amino acid residues. The (nonpolar) residues are shown in gray, while the (polar/charged) residues are shown in red.

Reactive structural elements

As mentioned above, adenylate kinase catalyzes the reaction ATP + AMP = 2ADP. The that interact with the substrate to accomplish this are shown in purple. The amino acids that comprise these residues are Arg, Asp, and Lys. However, the enzyme does not only interact with the ATP and AMP--it also interacts with (shown in red), a non-hydrolysable substrate with structural similarity to the enzyme's actual substrate. The , i.e. the residues that are in contact with the ligand, can be seen (cationic residues are shown in blue, whereas anionic residues are shown in bright red). Similar to the catalytic residues, which have positively-charged side chains, most of the side chains that interact with the ligand are also charged, although oxygen (primarily from Thr side chains) interacts with it as well. Furthermore, the carbonyl and nitrogen parts of the amino acid backbone also interact with the ligand. NOTE: The highlighted contact residues are actually those that are within 4 angstroms of the ligand, and all of them may not actually be in contact with it (although most of them are).

Water Accessibility

Of course, this enzyme is not reacting with its substrate or ligand in a vacuum, but rather in solvent, such as water. However, the molecule has a specific (water is shown in blue, the enzyme shown in white, and the ligand is shown in red). Because of the protein's folding, the solvent can't interact with every part of it; usually the outside is covered in solvent molecules, while the inside has less interaction with the solvent. It should be noted, however, that even some of the are in contact with the solvent.