The Molecule of the Month series, by David S.
Goodsell, explores the functions and
significance of selected biological macromolecules for a general
audience. These installments are available
here. A sample of the molecules featured during this past quarter are included below:
Alpha (top), beta, and gamma forms of carbonic anhydrase;
PDB entries 1ca2, 1ddz, and 1thj, respectively.
PDB ID: 1ca2
Eriksson, A. E., Jones, T. A., Liljas, A.: Refined structure of human carbonic anhydrase II at 2.0 ? resolution. Proteins (1988) 4: 274.
PDB ID: 1ddz
Mitsuhashi, S., Mizushima, T., Yamashita, E., Miyachi, S., Tsukihara, T.: X-Ray Structure of Beta-Carbonic Anhydrase from the Red Alga, Porphyridium purpureum,
Reveals a Novel Catalytic Site for CO2 Hydration J.Biol.Chem. (2000) 275: 5521.
PDB ID: 1thj
Kisker, C., Schindelin, H., Alber, B. E., Ferry, J. G., Rees, D. C. : A left-hand beta-helix revealed by the crystal structure of a carbonic anhydrase from the
archaeon Methanosarcina thermophila. EMBO J .(1996) 15: 2323.
January, 2004 -- Breathing is a fundamental function in life. In our lungs, oxygen diffuses into the blood, binds to hemoglobin, and is transported to all the cells of our body. Carbon dioxide is a byproduct of sugar and fat breakdown and must be removed from the body. However, less than 10% of the carbon dioxide that diffuses out of cells dissolves in the blood plasma, about 20% binds to hemoglobin, while 70% is converted to carbonic acid to be carried to the lungs.
Carbonic anhydrase, an enzyme in red blood cells, aids in the conversion of carbon dioxide to carbonic acid and bicarbonate ions. When red blood cells reach the lungs, the enzyme helps to convert the bicarbonate ions back to carbon dioxide, which we breathe out. Since its identification in 1933, carbonic anhydrase has been found abundant in all mammalian tissues, plants, algae, and bacteria. This ancient enzyme has three distinct classes -- alpha, beta, and gamma. While all three require a zinc ion at the active site, members of one class share very little sequence or structural similarity with the other two classes, suggesting that each class evolved independently.
Carbonic anhydrase from mammals belongs to the alpha class, the plant enzymes belong to the beta class, while the enzyme from methane-producing bacteria that grow in hot springs forms the gamma class. PDB entries 1ca2, 1ddz, and 1thj are examples of the alpha, beta, and gamma carbonic anhydrase enzymes, respectively. The zinc ions in the active sites are blue. The alpha enzyme is a monomer, while the gamma enzyme is trimeric. Although the beta enzyme is a dimer, there are four zinc ions bound to the structure indicating four possible enzyme active sites.
Since this enzyme produces and uses protons and bicarbonate ions, carbonic anhydrase plays a key role in the regulation of pH and fluid balance in different parts of our body. When there is a build up of the fluid that maintains the shape of our eyes, the fluid often presses on the optic nerve in the eye and may damage it. This condition is called glaucoma. In recent years, inhibitors of carbonic anhydrase have been used to
For more information about carbonic anhydrase, see
February, 2004 -- Glucose is a convenient high-energy fuel for cells because it is stable, soluble, and easy to transport from storage to where it's needed. Glycolysis (sugar breaking) is a ten-step cellular process to burn glucose in small, well-controlled steps to capture the energy as ATP (adenosine triphosphate).
A glucose molecule is primed with two phosphates (using up two ATP molecules), broken in two, reshaped, and dehydrated, forming four ATP molecules in the process, or a net gain of two ATPs. One glycolytic enzyme removes several hydrogen atoms from the sugar, transferring them to the small carrier molecule NAD (nicotinamide adenine dinucleotide). Many cells, including most of our own, eventually combine the hydrogens with oxygen to form water, building additional ATP in the process. In a reaction used to make wine and beer, yeast cells use alcohol dehydrogenase to add the hydrogen atoms back to the broken sugar molecule, forming alcohol. In extreme exercise, muscles add the hydrogen atoms back in a different way to form lactic acid.
For more information on glycolytic enzymes, see
This calcium pump in the membrane of the sarcoplasmic reticulum (PDB entry 1eul) allows muscles to relax by pumping calcium ions back into the sarcoplasmic reticulum.
Toyoshima, C., Nakasako, M., Nomura, H., Ogawa, H.: Crystal Structure of the Calcium Pump of Sarcoplasmic Reticulum at 2.6 ? Resolution. Nature (2000) 405: 647
March, 2004 -- Every time we move, our muscle cells use calcium ions to coordinate a massive molecular effort. These cells release a flood of calcium ions from a special intracellular container, the sarcoplasmic reticulum, which surrounds the bundles of actin and myosin filaments. The calcium ions rapidly spread and bind to tropomyosins on actin filaments. They shift shape slightly and allow myosin to bind and begin climbing up the filament, contracting the muscle.
The calcium pump, found in the membrane of the sarcoplasmic reticulum (right) from PDB entry 1eul, allows muscles to relax after this frenzied wave of calcium-induced contraction by pumping calcium ions back into the sarcoplasmic reticulum. This allows the muscle to relax. The pump has a big domain poking out of the sarcoplasmic reticulum, and a region that is embedded in the membrane, forming a tunnel to the other side. For each ATP broken, the pump transfers two calcium ions (blue spheres) through the membrane, and two or three hydrogen ions in the opposite direction.
For more information about the calcium pump, see
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.