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PDB Molecules of the Quarter: Anthrax Toxin, Penicillin-binding Proteins, and Glutamine Synthetase

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: 1acc (left)
Petosa, C., Collier, R. J., Klimpel, K. R., Leppla, S. H., Liddington, R. C.: Crystal structure of the anthrax toxin protective antigen. Nature 385 pp. 833 (1997)

PDB ID: 1k90 (center)
Drum, C. L., Yan, S.-Z., Bard, J., Shen, Y.-Q., Lu, D., Soelaiman, S., Grabarek, Z., Bohm, A., Tang, W.-J.: Structural Basis for the Activation of Anthrax Adenylyl Cyclase Exotoxin by Calmodulin Nature 415 pp. 396 (2002)

PDB ID: 1jky (right)
Pannifer, A. D., Wong, T. Y., Schwarzenbacher, R., Renatus, M., Petosa, C., Bienkowska, J., Lacy, D. B., Collier, R. J., Park, S., Leppla, S. H., Hanna, P., Liddington, R. C.: Crystal Structure of the Anthrax Lethal Factor Nature 414 pp. 229 (2001)

Anthrax Toxin: A Lethal Combination

April, 2002 -- Anthrax is a household word, in spite of the fact that anthrax is not a common disease. For humans, anthrax is difficult to contract. It is not transmitted from person to person--it is usually contracted when people come into contact with infected animals or their products. But recently, anthrax has gained the potential to be a major threat through bioterrorism. It is an effective weapon because it forms sturdy spores that may be stored for years, that rapidly lead to lethal infections when inhaled.

Anthrax is caused by an unusually large bacterium, Bacillus anthracis. Once its spores lodge in the skin or in the lungs, it rapidly begins growth and produces a deadly three-part toxin. These toxins are designed for maximum lethality, and are frighteningly effective. Part of the toxin is a delivery mechanism that seeks out cells; another part is a toxic enzyme that rapidly kills the cell. In anthrax toxin, there is one delivery molecule, termed "protective antigen" because of its use in anthrax vaccines (shown on the left from PDB entry 1acc). It delivers the other two parts, edema factor and lethal factor (center and right, from PDB entries 1k90 and 1jky), which are the toxic components that attack cells.

These types of multiple-part toxins are quite common in the bacterial world because they are exquisitely effective. Many other examples, such as toxins from the bacteria that cause cholera and whooping cough, may be found in the PDB. The delivery component specifically seeks out cell surfaces and inserts the toxic component where it can do the most damage. The toxic component is far more effective than poisons like cyanide and arsenic. Those poisons attack one-on-one, with a single cyanide molecule poisoning a single protein molecule. But toxic enzymes are compact cell-killing machines. Once inside the cell, they hop from molecule to molecule, destroying each in turn. These molecules are so effective that in some cases a single molecule can kill an entire cell.

Penicillin-binding Proteins: Magic Bullets

PDB ID: 3pte
Kelly, J. A., Knox, J. R., Zhao, H., Frere, J. M., Ghaysen, J. M.: Crystallographic mapping of beta-lactams bound to a D-alanyl-D-alanine peptidase target enzyme. J Mol Biol 209 pp. 281 (1989)

May, 2002 -- Bacteria pose a continual threat of infection, both to humans and to other higher organisms. Thus, when looking for new ways to fight infection, it is often productive to look at how other plants, animals and fungi protect themselves. This is how penicillin was discovered. Through a chance observation in 1928, Alexander Fleming discovered that colonies of Penicillium mold growing in his bacterial cultures were able to stave off infection. With more study, he found that the mold was flooding the culture with a molecule that killed the bacteria, penicillin.

Penicillin and other beta-lactam antibiotics (named for an unusual, highly reactive lactam ring) are very efficient and have few side effects (apart from allergic reactions in some people). This is because the penicillin attacks a process that is unique to bacteria and not found in higher organisms. As an additional advantage, the enzymes attacked by penicillin are found on the outside of the cytoplasmic membrane that surrounds the bacterial cell, so the drugs can attack directly without having to cross this strong barrier.

When treated with low levels of penicillin, bacterial cells change shape and grow into long filaments. As the dosage is increased, the cell surface loses its integrity, as it puffs, swells, and ultimately ruptures. Penicillin attacks enzymes that build a strong network of carbohydrate and protein chains, called peptidoglycan, that braces the outside of bacterial cells. Bacterial cells are under high osmotic pressure; because they are concentrated with proteins, small molecules and ions are on the inside and the environment is dilute on the outside. Without this bracing corset of peptidoglycan, bacterial cells would rapidly burst under the osmotic pressure.

Penicillin is chemically similar to the modular pieces that form the peptidoglycan, and when used as a drug, it blocks the enzymes that connect all the pieces together. As a group, these enzymes are called penicillin-binding proteins. Some assemble long chains of sugars with little peptides sticking out in all directions. Others, like the D-alanyl-D-alanine carboxypeptidase/transpeptidase shown here (PDB entry3pte), then crosslink these little peptides to form a two-dimensional network that surrounds the cell like a fishing net.

Glutamine Synthetase

PDB ID: 1fpy
Gill, H. S., Eisenberg, D.: The Crystal Structure of Phosphinothricin in the Active Site of Glutamine Synthetase Illuminates the Mechanism of Enzymatic Inhibition Biochemistry 40 pp. 1903 (2001)
June, 2002 -- Our cells are continually faced with a changing environment. Think about what you eat. Some days you might eat a lot of protein, other days you might eat a lot of carbohydrate. Sometimes you may eat nothing but chocolate. Your body must be able to respond to these different foods, producing the proper enzymes for capturing the nutrients in each. The same is doubly true for small organisms like bacteria, which do not have as many options in choosing their diet. They must eat whatever food happens to be close by, and then mobilize the enzymes needed to use it.

The enzyme glutamine synthetase is a key enzyme controlling the use of nitrogen inside cells. Glutamine, as well as being used to build proteins, delivers nitrogen atoms to enzymes that build nitrogen-rich molecules, such as DNA bases and amino acids. So, glutamine synthetase, the enzyme that builds glutamine, must be carefully controlled. When nitrogen is needed, it must be turned on so that the cell does not starve. But when the cell has enough nitrogen, it needs to be turned off to avoid a glut.

Glutamine synthetase acts like a tiny molecular computer, monitoring the amounts of nitrogen-rich molecules. It watches levels of amino acids like glycine, alanine, histidine and tryptophan, and levels of nucleotides like AMP and CTP. If too much of one of these molecules is made, glutamine synthetase senses this and slows production slightly. But as levels of all of these nucleotides and amino acids rise, together they slow glutamine synthetase more and more. Eventually, the enzyme grinds to a halt when the supply meets the demand.

The glutamine synthetase molecule shown here (PDB entry 1fpy) is from bacteria. It is composed of twelve identical subunits, each of which has an active site for the production of glutamine. When performing its reaction, the active site binds to glutamate and ammonia, and also to an ATP molecule that powers the reaction. But, the active sites also bind weakly to other amino acids and nucleotides, partially blocking the action of the enzyme. All of the many sites communicate with one another, and as the concentrations of competing molecules rise, more and more of the sites are blocked, eventually shutting down the whole enzyme. The cell has a more direct approach when it wants to shut down the enzyme. At a key tyrosine next to the active site, an ADP molecule can be attached to the protein, completely blocking its action.

We make several versions of glutamine synthetase in our own cells. Most of our cells make a version similar to the bacterial one described here, but with eight subunits instead of twelve. Like the bacterial enzyme, it is controlled by the nitrogen-rich compounds down the synthetic pipeline. We also make a second glutamine synthetase in our brain. There, glutamate is used as a neurotransmitter, and glutamine synthetase is used when the glutamate is recycled after a nerve impulse is delivered. In the brain, glutamine synthetase is in constant action, so a highly-regulated version is not appropriate. Instead, the alternate form is active all the time, continually performing its essential duty.