Molecule of the Month: Ribonucleotide Reductase

DNA and RNA are almost identical in structure, but one small difference has big consequences. A single oxygen atom, which is missing in each DNA nucleotide, distinguishes DNA from RNA. While small, this missing oxygen makes DNA more stable, making it a good molecule for long-term storage of information. On the other hand, RNA is less stable. The hydroxyl group formed by the extra RNA oxygen makes it more susceptible to hydrolysis, so RNA often acts as a biological “flash drive,” storing temporary biological data that is discarded when no longer needed. The only way of creating deoxyribonucleotides in our bodies is from ribonucleotides using the enzyme ribonucleotide reductase, which is essential for DNA synthesis and repair.

The catalytic mechanism of ribonucleotide reductase is interesting because it requires free radicals. While free radicals are usually harmful for our bodies, in ribonucleotide reductase they play an essential role in production of the building blocks of DNA. For Class I forms of the enzyme, a free radical is produced in the beta subunit (also called R2), and then travels to the larger catalytic alpha subunit (or R1) where production of deoxyribonucleotides occurs. While ribonucleotide reductase is a highly conserved enzyme across all forms of life, there are many different classes that use different metals to generate these essential free radicals. The active form of a well-studied bacterial ribonucleotide reductase, shown here from PDB entries 1mrr and 3r1r, has two copies of each subunit connected by a flexible tether.

Ribonucleotide reductase is an important target for anticancer drugs. One way of stopping the growth of cancer cells is to shut down the enzymes involved in DNA synthesis. The obvious way of inhibiting this enzyme would be to create a molecule that looks like a nucleoside and blocks binding of normal nucleoside diphosphates in the active site. However, because nucleoside analogues are very similar to actual nucleosides used in the cell, they may be incorporated into DNA made by healthy cells as well as cancer cells, which results in bad side effects. One way of fixing this problem is making small molecules that are not nucleoside analogues, but still selectively block ribonucleotide reductase. Examples of both approaches are included below in “Exploring the Structure.”

Because ribonucleotide reductase is essential for DNA synthesis, it is highly regulated in the cell and only works when necessary. When the concentration of ATP in the cell is high, ATP binds to ribonucleotide reductase as a signal to make more deoxyribonucleotides. This usually happens during cell division, as a lot of new DNA is created at that time. Besides that, ribonucleotide reductase has a separate site that senses which deoxyribonucleotides are required. To prevent the enzyme from making toxic levels of deoxyribonucleotides, dATP binds to the enzyme and shuts it down. The way the enzyme shuts down is very clever: as seen in PDB entry 3uus, multiple subunits of the enzyme bind to each other, creating a ring structure. This molecular rearrangement disrupts the pathway for the free radical to travel from the beta subunit to the alpha subunit.