Ribonucleotide Reductase

Ribonucleotide reductase creates the building blocks of DNA

Escherichia coli ribonucleotide reductase forms a tetramer with two alpha subunits (blue) and two beta subunits (green). A nucleotide (red) is bound in a regulatory site in this structure.
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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.

Radical Enzyme

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.

Target for Cancer Treatment

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.”

Inhibited state of ribonucleotide reductase.
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Checks and Balances

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.

Exploring the Structure

Ribonucleotide Reductase

Structures of ribonucleotide reductase inhibited by two synthetic molecules are shown here (PDB entries 5tus and 2eud). Gemcitabine is a nucleoside-analogue anti-cancer prodrug that is currently used to treat various types of cancer. Gemcitabine inhibits the alpha subunit by binding to the catalytic site and “tricking” the enzyme by having fluoride atoms where a hydrogen atom and a hydroxyl group are supposed to be in the regular nucleoside. Naphthyl salicylic acyl hydrazone (NSAH) is a non-nucleoside inhibitor discovered by in silico screening. It also binds in the catalytic site and inhibits ribonucleotide reductase reversibly. To compare these structures in more detail, click on the image for an interactive JSmol.

Topics for Further Discussion

  1. Many other proteins are targets for cancer chemotherapy--you can look at the PDB-101 Category on Cancer to see some of them.
  2. There are many structures of both DNA and RNA in the PDB archive--try looking for the hydroxyl group on each RNA sugar that makes the difference. PDB entry 1g4q is an easy place to start--it includes a short hybrid double helix with one DNA strand and one RNA strand.

References

  1. 5tus: Ahmad, M.F., Alam, I., Huff, S.E., Pink, J., Flanagan, S.A., Shewach, D., Misko, T.A., Oleinick, N.L., Harte, W.E., Viswanathan, R., Harris, M.E., Dealwis, C.G. (2017) Potent competitive inhibition of human ribonucleotide reductase by a nonnucleoside small molecule. Proc. Natl. Acad. Sci. U.S.A. 114: 8241-8246
  2. 3uus: Ando, N., Brignole, E.J., Zimanyi, C.M., Funk, M.A., Yokoyama, K., Asturias, F.J., Stubbe, J., Drennan, C.L. (2011) Structural interconversions modulate activity of Escherichia coli ribonucleotide reductase. Proc.Natl.Acad.Sci.USA 108: 21046-21051
  3. 2eud: Xu, H., Faber, C., Uchiki, T., Racca, J., Dealwis, C. (2006) Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly. Proc.Natl.Acad.Sci.Usa 103: 4028-4033
  4. 3r1r: Eriksson, M., Uhlin, U., Ramaswamy, S., Ekberg, M., Regnstrom, K., Sjoberg, B.M., Eklund, H. (1997) Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding. Structure 5: 1077-1092
  5. 1mrr: Atta, M., Nordlund, P., Aberg, A., Eklund, H., Fontecave, M. (1992) Substitution of manganese for iron in ribonucleotide reductase from Escherichia coli. Spectroscopic and crystallographic characterization. J.Biol.Chem. 267: 20682-20688

October 2019, David Goodsell, Galyna Khramova

doi:10.2210/rcsb_pdb/mom_2019_10
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. More