No. 16
Winter 2003

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PDB Molecules of the Quarter: Dihydrofolate Reductase, Ferritin and Transferrin, and Cytochrome c

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PDB Molecules of the Quarter: Dihydrofolate Reductase, Ferritin and Transferrin, and Cytochrome c

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: 7dfr
Bystroff, C., Oatley, S. J., Kraut, J. (1990): Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state. Biochemistry 29, p. 3263.
Dihydrofolate Reductase: A Target in the Fight Against Cancer

October, 2002 -- Dihydrofolate reductase is a small enzyme that plays a supporting role, but an essential role, in the building of DNA and other processes. It manages the state of folate, a snaky organic molecule that shuttles carbon atoms to enzymes that need them in their reactions. Of particular importance, the enzyme thymidylate synthase uses these carbon atoms to build thymine bases, an essential component of DNA. After folate has released its carbon atoms, it has to be recycled. This is the job performed by dihydrofolate reductase.

Dihydrofolate reductase, shown in PDB entry 7dfr, juggles two relatively large molecules in its reaction. It has a long groove that binds to folate at one end, and to NADPH at the other end. The protein wraps sidechains around the two molecules, positioning them tightly next to one another. Then, the enzyme transfers hydrogen atoms from NADPH to the folate, converting folate to a useful reduced form.

Enzymes with essential roles are sensitive targets for drug therapy. Dihydrofolate reductase was the first enzyme to be targeted for cancer chemotherapy. The first drug used for cancer chemotherapy was aminopterin. It binds to dihydrofolate reductase a thousand times more tightly than folate, blocking the action of the enzyme. Today, methotrexate and other variations on aminopterin are used, because of their tighter binding and better clinical characteristics. Since these drugs attack a key step in the production of DNA, they tend to kill cells that are actively growing rather than cells that are not growing. Since cancer cells are often the most rapidly reproducing cells in a patient, the drug will have the strongest effect on the cancer cells. The side effects of chemotherapy, however, are the result of the drug on other normally-growing tissues, such as hair follicles and the lining of the stomach.

Further information about dihydrofolate reductase can be found at http://www.rcsb.org/pdb/molecules/pdb34_2.html.


Ferritin and Transferrin: Iron Storage and Transport

PDB ID: 1fha
Lawson, D. M., Artymiuk, P. J., Yewdall, S. J., Smith, J. M., Livingstone, J. C., Treffry, A., Luzzago, A., Levi, S., Arosio, P., Cesareni, G., et al. (1991): Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature 349, p. 541.

November, 2002 -- Iron is found everywhere on the Earth, so it is no surprise that living cells use iron ions in many ways. We use iron throughout our body, for many tasks. Iron ions bind strongly and specifically to small molecules such as oxygen, making it an essential tool for manipulating these elusive molecules. Iron ions also cycle easily between the ferrous and ferric forms, providing a handy tool for manipulating individual electrons. Iron ions, however, pose a great challenge in our modern biological environment. The water filling cells and the oxygen in the air together conspire to convert iron ions to the ferric state, which is highly insoluble, forming rust-like oxides. The cell must somehow shelter iron ions so that they may be stored and delivered in the necessary quantities. This is the job of ferritin and transferrin.

Inside cells, extra iron ions are locked safely in the protein shell of ferritin, shown in PDB entry 1fha. Ferritin is composed of 24 identical protein subunits that form a hollow shell. After entering the ferritin shell, iron ions are converted into the ferric state, where they form small crystallites along with phosphate and hydroxide ions. There is room to pack about 4500 iron ions inside.

We have about 3.7 grams of iron in our body, painstakingly gathered from iron in our diet. About 2.5 grams are locked inside the hemoglobin in our blood, where they assist in the transport of oxygen. This is a valuable and essential resource, so special mechanisms for the recycling of this iron have been developed. Another few tenths of a gram are found in myoglobin, which also assists in oxygen management. A remarkably small amount--about 0.02 g--is distributed between the many different proteins that transfer electrons, such as the proteins of the electron transport chain that create most of our cellular ATP supplies. The rest, about a gram, is stored inside ferritin to fulfill future needs.

Iron ions are delivered in the blood by the protein transferrin, shown in PDB entry 1h76. Each transferrin molecule can carry two iron ions, with each ion coupled with a carbonate ion. The protein contains an array of amino acids that are perfectly arranged to form four bonds to the iron ion, which locks it in place. Once it finds its iron atoms, transferrin flows through the blood until it finds a transferrin receptor on the surface of a cell. PDB entry 1cx8 contains coordinates for the part of the receptor that is outside the cell. Transferrin binds tightly to the receptor and is drawn into the cell in a small vesicle. The cell then acidifies the inside of this little pocket, which causes transferrin to release its iron. Then, the receptor and empty transferrin are recycled back to the outside of the cell. Triggered by the neutral pH of the blood, the receptor releases the empty transferrin, and it continues its job of gathering iron.

Further information about ferritin and transferrin can be found at http://www.rcsb.org/pdb/molecules/pdb35_2.html.


Cytochrome c: Delivering Electrons

PDB ID: 3cyt
Takano, T., Dickerson, R. E. (1980): Redox conformation changes in refined tuna cytochrome c. Proc. Natl. Acad. Sci. U S A 77, p. 6371.

December, 2002 -- Electricity is a common phenomenon in our modern world, powering everything from the lights in your room to the computer in front of you. Electricity is the flow of electrons within a conductive material, such as metal wires. These electrons flow in bulk, meandering from atom to atom along the wire. Cells also use electricity to power many processes, but the electrons move in a very different way. The electrons do not flow smoothly along a cell-sized wire. Instead, electrons are transported one at a time, jumping from protein to protein. In this way, the electrons may be picked up from one particular place and delivered exactly where they are needed.

Cytochrome c, shown in PDB entry 3cyt, is a carrier of electrons. Like many proteins that carry electrons, it contains a special prosthetic group that handles the slippery electrons. Cytochrome c contains a heme group with an iron ion gripped tightly inside. The iron ion readily accepts and releases an electron. The surrounding protein creates the perfect environment for the electron, tuning how tightly it is held. The protein also determines where cytochrome c fits into the overall cellular electronic circuit.

Cytochrome c is an ancient protein, developed early in the evolution of life. Since this essential protein performs a key step in the production of cellular energy, it has changed little in millions of years. So, you can look into yeast cells or plant cells or our own cells and find a very similar form of cytochrome c. If you look around the PDB, however, you can find a diverse collection of other electron carrier molecules. There are many variations on cytochrome c, which use heme and iron to carry electrons, but change the protein surrounding them to perform different jobs. Other carriers use other prosthetic groups to carry electrons, such as clusters of iron and sulfur (such as ferredoxin), brilliant blue copper ions (such as azurin and plastocyanin) or more exotic metal ions. Like cytochrome c, each of these proteins is a single connection in a cellular electronic circuit, transferring electrons from one point to another.

Further information about cytochrome c can be found at http://www.rcsb.org/pdb/molecules/pdb36_2.html.