Sandbox 50

From Proteopedia

Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013.

1 Description
2 Structure
3 Hydrophobic and Hydrophilic Residues
4 Active Site
5 Solvent
6 References

Description

Adenylate Kinase, also known as ADK, is an phosphotransfer enzyme that catalyzes the reversible transfer of phosphate between ATP and AMP. It plays an important role in cell maintenance and cell growth being involved with energy metabolism, signaling, and nucleotide synthesis. The reaction that takes place during the catalysis is ATP + AMP = 2ADP. The enzyme has two conformations, where the inactive form is open, and the active form is closed. The open conformation allows substrates to bind, and the closed form is when the substrate is already bound, and the catalysis is taking place. The enzyme is found in various organisms, and the following images shows the structure of Adenylate Kinase from Yersinia pestis, also known as yeast.

Structure

Adenylate Kinase is made up of 214 amino acids, and the of the protein can be seen on the right in light blue surrounding the non-hydrolysable substrate analogue (red). The of the protein contains 12 alpha helices (yellow) and 7 beta sheets (green). This secondary structure is held together by , which are anti-parallel between the beta sheets. This hydrogen bond network also assists in the flexibility of the enzyme.

Hydrophobic and Hydrophilic Residues

The of ADK, seen in gray, is buried in the interior of the protein. While the , all the charged and polar side chains (purple), are on the surface of the protein and exposed. The location of the residues depend on the solvent and the environment that the protein is found in. All the hydrophobic residues aggregate together, and bury themselves in the interior of the protein to minimize their contact with their environment. The hydrophilic residues, on the other hand, is exposed on the surface because the enzyme is in an hydrophilic environment. Although, most of the hydrophilic residues would be exposed, it is possible for some of the to be buried in the interior, but they would interact with each other be stabilized there. There are also hydrophilic residues in the active site of the enzyme.

Active Site

The active site, like mentioned above, is where the substrates binds to the enzyme to be catalyzed. In ADK, the (gray, blue, pink), is in the interior of the protein. The pink is where the ligand binds directly. There are mostly hydrophilic residues present in the active site because water enters the active site regularly it causes the hydrophobic residues to still be buried within the protein. But there are some hydrophobic interactions that take place between the enzyme and the substrates, which helps stabilizes the substrate in the site, so that it can be catalyzed. There are six , which are highlighted black on the image, and they are specifically involved in the catalyzes of the substrates forming hydrogen bonds with the substrate. The catalytic residues are all charged residues and include Lysine, Aspartic acid, and Arginine. These residues also allow for electrostatic interactions but can be effected by the presence of the water in the active site.

Solvent

The , which is water (blue), can be co-crystallized with the enzyme. The water can be found all around the protein but there is also some water molecules in the active site, around the ligand. This further indicates why the hydrophilic residues are found on the surface, and the nonpolar residues are buried away. The water creates a hydrophilic environment, and the hydrophobic residues aggregate together in the interior, which is the hydrophobic effect and drives the water out. So for the most part, there are not water molecules in between the secondary structure, but there are some water molecules in the open spaces between the backbone.The hydrophilic residues in the active site allow water to be present, and also make it easier for the substrates to enter and facilitates in the catalysis.