Go to the National Center for Biotechnology Information (NCBI: www.ncbi.nlm.nih.gov/) and click on the word Structure along the menu line (last word on the right). If you choose to download the Cn3D program, you will be able to view the three-dimensional structures directly from the links after you have done a search for a protein structure. While Cn3D is not as powerful as some of the programs discussed in the text, it is a very handy tool. In the search box, type in "cam kinase" for calmodulindependent kinase and observe the output. Protein kinases are enzymes (transferases) that transfer a phosphate from ATP to another protein. This covalent modification results in structural changes that either activate or inhibit enzyme activity. Hence, protein kinases are regulatory enzymes in the cell (see Chapter 13).
(a) Click on 2V7O. This brings up the MMDB Structure Summary page. What kinds of information can you find here?
(b) This site recognizes two structural domains in calcium-calmodulin-dependent kinase. What structural features seem to dominate each domain?
(c) Go back to the Structure Summary page, and click on VAST (Vector Alignment Search Tool). Click on each domain and examine the proteins that are retrieved, which show similar structures (this information is based on available 3D structural information). Are any hits for either domain not protein kinases?