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. |
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Contents |
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, ATP + AMP = 2ADP, 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.
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, where the ligand binds, to help it enter so that the reaction can take place.
Active Site
The active site, like mentioned above, is where the ligand/substrate binds to the enzyme to be catalyzed. In ADK, the (gray, blue, pink), is in the interior of the protein. There are also six , which are specifically involved in the catalyzes of the substrates, and they are highlighted black on the image.
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, and in between the secondary structure of the enzyme. This further indicates why the hydrophilic residues are found on the surface, and the nonpolar residues are buried away. There are also hydrophilic residues in the active site, which is why water is also present there.
