PDB Molecules of the Quarter: p53 Tumor Suppressor, Chaperones, and Reverse Transcriptase

The Molecule of the Month series explores the functions and significance of selected biological macromolecules for a general audience. These features, written and illustrated by Dr. David S. Goodsell of the Scripps Research Institute, are available at http://www.rcsb.org/pdb/molecules/molecule_list.html. A sample of the molecules featured during this past quarter are included below:

PDB ID: 1olg
Takano, K., Yamagata, Y., Fujii, S., Yutani, K. (1997): Contribution of the hydrophobic effect to the stability of human lysozyme: calorimetric studies and X-ray structural analyses of the nine valine to alanine mutants. Biochemistry 36, pp. 688.

PDB ID: 1tup
Cho, Y., Gorina, S., Jeffrey, P. D., Pavletich, N. P. (1994): Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science 265, pp. 346.

PDB ID: 1ycq
Kussie, P. H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A. J., Pavletich, N. P. (1996): Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274, pp. 948.

p53 Tumor Suppressor: Guardian of the Cell

July, 2002 -- Our cells face many dangers, including chemicals, viruses, and ionizing radiation. If cells are damaged in sensitive places by these attackers, the effects can be disastrous. For instance, if key regulatory elements are damaged, the normal controls on cell growth may be blocked and the cell will rapidly multiply and grow into a tumor. p53 tumor suppressor is one of our defenses against this type of damage. p53 tumor suppressor is normally found at low levels, but when DNA damage is sensed, p53 levels rise and initiate protective measures. p53 binds to many regulatory sites in the genome and begins production of proteins that halt cell division until the damage is repaired. Or, if the damage is too severe, p53 initiates the process of programmed cell death, or apoptosis, which directs the cell to commit suicide, permanently removing the damage.

p53 tumor suppressor is a flexible molecule composed of four identical protein chains. Flexible molecules are difficult to study by X-ray crystallography because they do not form orderly crystals, and if they do crystallize, the experimental images are often blurry. So, p53 has been studied in parts, by removing the flexible regions and solving structures of the pieces that form stable structures. Three of these compact, globular portions, termed "domains", have been studied. At the center of p53 is a tetramerization domain (PDB entry 1olg) that ties the four chains together. A long flexible region in each chain then connects to the second stable domain: a large DNA-binding domain (PDB entry 1tup) that is rich in arginine residues that interact with DNA. This domain recognizes specific regulatory sites on the DNA. The third stable domain studied thus far is the transactivation domain (PDB entry 1ycq), found near the end of each arm, that activates the DNA-reading machinery.

As you might guess from its name, p53 tumor suppressor plays a central role in the protection of your body from cancer. Cancer cells typically contain two types of mutations: mutations that cause uncontrolled growth and multiplication of cells, and other mutations that block the normal defenses that protect against unnatural growth. p53 is in this second category and mutations in the p53 gene contribute to about half of the cases of human cancer. Most of these are missense mutations, changing the information in the DNA at one position and causing the cell to build p53 with an error, swapping an incorrect amino acid at one point in the protein chain. In these mutants, the normal function of p53 is blocked and the protein is unable to stop multiplication in the damaged cell. If the cell has other mutations that cause uncontrolled growth, the cell will develop into a tumor.

Further information about p53 tumor suppressor can be found at http://www.rcsb.org/pdb/molecules/pdb31_2.html.

Chaperones: Guides Along the Folding Pathway

PDB ID: 1aon
Xu, Z., Horwich, A. L., Sigler, P. B. (1997) : The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature 388, pp. 741.

August, 2002 -- As you can see when looking through the many structures in the PDB, most active proteins have a stable, globular structure. However, proteins are built as formless chains, pieced together one amino acid at a time by ribosomes. Most protein chains then fold spontaneously into their final structure, driven by the need to shelter their carbon-rich portions from the surrounding water. But some--large proteins or proteins with several domains--need some assistance. As they fold into a compact shape, they might get stuck somewhere along the way.

This is not a trivial problem. Cells cannot merely wait for proteins to fold properly. Misfolded proteins often have carbon-rich amino acids on their surfaces, instead of tucked safely inside. These carbon-rich patches associate strongly with similar patches on other proteins, forming large aggregates. Random aggregates are death to cells: diseases such as sickle cell anemia, mad cow disease, and Alzheimer's disease are caused by unnatural aggregations of proteins into cell-clogging fibrils.

Chaperones are proteins that guide proteins along the proper pathways for folding. They protect proteins when they are in the process of folding, shielding them from other proteins that might bind and hinder the process. Many chaperone proteins are termed "heat shock" proteins (with names like HSP-60) because they are made in large amounts when cells are exposed to heat. Heat, in general, destabilizes proteins and makes misfolding more common. So when it gets really hot, cells need some extra help with their proteins.

One impressive type of chaperone forms an enclosed environment for folding proteins which totally protects them as they fold. The GroEL-GroES complex of the bacterium E. coli can be seen in PDB entry 1aon. It is composed of two stacked rings of GroEL proteins, and a cap on one side composed of GroES. Seven GroEL proteins form a ring with a protein-sized cavity inside. Unfolded proteins enter this cavity and fold up inside.

Further information about chaperones can be found at http://www.rcsb.org/pdb/molecules/pdb32_2.html.

Reverse Transcriptase: A Sloppy Enzyme

PDB ID: 3hvt
Wang, J., Smerdon, S. J., Jager, J., Kohlstaedt, L. A., Rice, P. A., Friedman, J. M., Steitz, T. A. (1994): Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer. Proc. Natl. Acad. Sci. U.S.A. 91, pp. 7242.

September, 2002 -- Viruses are tricky. They use all sorts of unusual mechanisms during their attacks on cells. HIV is no exception. It is a retrovirus, which means that it has the ability to insert its genetic material into the genome of the cells that it infects. But, infectious HIV particles carry their genome in RNA strands. Somehow, during infection, the virus needs to make a DNA copy of its RNA genome. This is very unusual, because all of the normal cellular machinery is designed to make RNA copies from DNA, but not the reverse. DNA is normally only created using other DNA strands as a template. This tricky reversal of synthesis is performed by the enzyme reverse transcriptase, as found in PDB entry 3hvt. Inside its large, claw-shaped active site, it copies the HIV RNA and creates a double-stranded DNA version of the viral genome. This then integrates into the cell's DNA, and later instructs the cell to make additional copies of the virus.

Viruses are tiny. They only carry enough genetic material to encode a few proteins. Many viruses, such as poliovirus and rhinovirus, carry the bare minimum--just enough to specify their own structure and get synthesis started once they get inside cells. The genome of HIV, on the other hand, carries instructions for building a few enzymes that are used in the reproduction of the virus. Reverse transcriptase is one of these enzymes. But, space in the HIV genome is still at a premium, so reverse transcriptase is encoded in a tricky way. It is composed of two different subunits, but both are encoded by the same gene. After the protein is made, one of the subunits is clipped to a smaller size so that it can form the proper mate with one full-sized subunit.

Reverse transcriptase performs a remarkable feat, reversing the normal flow of genetic information, but it is rather sloppy in its job. The polymerases used to make DNA and RNA in cells are very accurate and make very few mistakes. This is essential because they are the caretakers of our genetic information, and mistakes may be passed on to our offspring. Reverse transcriptase, on the other hand, makes lots of mistakes, up to about one in every 2,000 bases that it copies (if this same error rate occurred in the "Molecule of the Month," there would be two typos in this month's installment). You might think that this would cause severe problems. But, in fact, this high error rate turns out to be an advantage for the virus in this era of drug treatment. The errors allow HIV to mutate rapidly, finding drug resistant strains in a matter of weeks after treatment begins. Fortunately, the recent development of treatments that combine several drugs are often effective in combating this problem. Since the virus is simultaneously attacked by several different drugs, it cannot mutate to evade all of them at the same time.

Further information about reverse transcriptase can be found at http://www.rcsb.org/pdb/molecules/pdb33_2.html.