Structural View of Biology
Enzymes are Nature's chemists, performing all of the chemical transformations needed for life. Enzymes catalyze chemical reactions by bringing together all of the necessary chemical tools in the proper place. They typically have an "active site" that captures the chemicals that will be modified, holding them in the perfect orientation to perform the chemical change. Researchers have separated the many types of enzymes into a few functional classes, based on the reactions that they perform. Click on any of the sub-categories below to explore a few examples of each enzyme class. You can also explore many other enzymes in the other functional categories in "Structural View of Biology."
Ribozymes - Enzymes Made of RNA
Most enzymes are built of protein, but several RNA enzymes have also been discovered. Ribozymes typically perform reactions on other RNA molecule, cleaving themselves or other strands, but they also perform other important reactions, such as the reaction that connects amino acids in the ribosome.
Scroll to a Molecule of the Month Feature in this subcategory:
Protein synthesis is the major task performed by living cells. For instance, roughly one third of the molecules in a typical bacterial cell are dedicated to this central task. Protein synthesis is a complex process involving many molecular machines. You can look at many of these molecules in the PDB, including DNA, DNA polymerases, and RNA polymerases; a host of repressors, DNA repair enzymes, topoisomerases, and histones; tRNA and acyl-tRNA synthetases; and molecular chaperones. This month, for the first time, you can also look at the factory of protein synthesis in atomic detail.
Ribosomes are one of the wonders of the cellular world, and one of the many wonders you can explore yourself at the RCSB PDB. In 2000, structural biologists Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath made the first structures of ribosomal subunits available in the PDB, and in 2009, they each received the Nobel Prize for this work. Structures are also available for many of the other players in protein synthesis, including transfer RNA and elongation factors. Building on these structures, there are now hundreds of structures of entire ribosomes in the PDB, revealing the atomic details of many important steps in protein synthesis.
Nature is full of surprises, and you can be sure that once you think you understand something, Nature will come up with an exception. Twenty years ago, this was the case with enzymes. After decades of work, biochemists thought that proteins were the only molecules that catalyzed chemical reactions in the cell, so it came as a surprise when Thomas Cech and his coworkers discovered a natural RNA splicing reaction that occurs even when all of the proteins are removed. Since then, researchers have discovered many additional examples of ribozymes--RNA molecules that perform chemical tasks.
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