January 1, 2002
PDB Molecules of the Quarter: Photosystem I, DNA, and Glycogen Phosphorylase
The Molecule of the Month series is a wonderful collection of short columns featuring a new PDB structure of interest each month. They describe the functions and significance of the selected biological macromolecules for a general audience, providing a basic understanding of structural interactions. Written and illustrated by Dr. David S. Goodsell of the Scripps Research Institute, this feature adds a unique aesthetic quality and informative educational resource to the PDB Web site. You can access the Molecule of the Month installations at http://www.rcsb.org/pdb/molecules/molecule_list.html.
Below is a sample of the information that was presented in this feature during the past quarter:
October, 2001 -- Look around. Just about everywhere that you go, you will see something green. Plants cover the Earth, and their smaller cousins, algae and photosynthetic bacteria, can be found in nearly every corner. Everywhere, they are busy converting carbon dioxide into sugar, creating living organic molecules out of air using the energy of sunlight as power. This process, termed photosynthesis, provides the material foundation on which all life rests.
At the center of photosynthesis is a class of proteins termed photosynthetic reaction centers. These proteins capture individual light photons and use them to provide power for building sugar. One example is photosystem I (PDB entry 1jb0), one of the two large reaction centers used in cyanobacteria, algae and plants. Photosystem I is a trimeric complex that forms a large disk. In cells, the complex floats in a membrane with the large flat faces exposed above and below the membrane.
Each of the three subunits of photosystem I is a complex of a dozen proteins, which together support and position over a hundred cofactors. Some of these cofactors are exposed around the edge of complex and many others are buried inside. Cofactors are small organic molecules that are used to perform chemical tasks that are beyond the capabilities of pure protein molecules. The cofactors in photosystem I include many small, brightly-colored molecules such as chlorophyll, which is bright green, and carotenoids, which are orange. The colors are, in fact, the reason that these molecules are useful: the colors are an indication that the cofactors absorb other colors strongly. For instance, chlorophyll absorbs blue and red light, leaving the beautiful greens for us to see. The energy from these absorbed colors is then captured to perform photosynthesis.
The heart of photosystem I is an electron transfer chain, a chain of chlorophyll, phylloquinone, and three iron-sulfur clusters. These cofactors convert the energy from light into energy that the cell can use. The two chlorophyll molecules at the bottom of the chain capture the light first. When they do, an electron is excited into a higher energy state. Normally this electron would quickly decay, releasing heat or releasing a new photon of slightly lower energy. But before this has a chance to happen, photosystem I passes this electron on, up the chain of cofactors. At the top, the electron is transferred to a small ferredoxin protein, which then ferries it on to the other steps of photosynthesis. At the bottom, the hole left by this wandering electron is filled by an electron from another protein, plastocyanin.
This may seem rather mundane until you see the trick that the photosystem is performing. The proteins at both ends of this process, ferredoxin and plastocyanin, are carefully chosen. Because of the special design of their own cofactors, it is more difficult to add an electron to ferredoxin than it is to plastocyanin--normally, the flow would be in the opposite direction. But photosystem I uses the energy from light to energize the electron, moving it in a difficult direction. Then, since the electron is placed in such an energetic position, it can be used to perform unfavorable duties such as the production of sugar from carbon dioxide.
Different photosystems are used by different photosynthetic organisms. Higher plants, algae, and some bacteria have photosystem I, and a second one termed photosystem II. A low resolution structure of photosystem II is available in PDB entry 1fe1. Photosystem II uses water instead of plastocyanin as the donor of electrons to fill the hole left when the energized electron is passed up the chain. When it grabs electrons from a water molecule, photosystem II splits the water and releases oxygen gas. This reaction is the source of all of the oxygen that we breathe. Some photosynthetic bacteria contain a smaller photosynthetic reaction center, such as the one in PDB entry 1prc. As in photosystem I, a stack of chlorophyll and other cofactors transfer a light-energized electron up to an energetic electron carrier.
Of course, plants do not rely on the slim chance of a photon running into one tiny chlorophyll molecule in the middle of the reaction center. As with all things in life, cells have found an even better way. Photosystem I contains an electron transfer chain at the center of each of the three subunits. Each one is surrounded by a dense ring of chlorophyll and carotenoid molecules that act as antennas. These antenna molecules each absorb light and transfer energy to their neighbors. Rapidly, all of the energy funnels into the three reaction centers, where is captured to create activated electrons.
You can view the many photosystem I cofactors of the electron transfer chain and the antenna in PDB entry 1jb0. Only one of the three subunits is included in the file, but you will find that this is complicated enough. Two special chlorophyll molecules, residues 1140 and 1239, act as a bridge between the reaction center in the middle and the many molecules in the surrounding antenna. Magnesium ions lie at the center of each chlorophyll. The residue numbers for the electron transfer chain are 1011-1013 and 1021-1023 for the chlorophylls, 2001-2002 for the phylloquinones, and 3001-3003 for the iron sulfur clusters.
A list of all photosystem I structures in the PDB as of October, 2001, is available at http://www.rcsb.org/pdb/molecules/pdb22_report.html. For more information about photosystem I, see http://www.rcsb.org/pdb/molecules/pdb22_6.html.
DNA: Your Inheritance
DNA is read-only memory, archived safely inside cells. Genetic information is stored in an orderly manner in strands of DNA. DNA is composed of a long linear strand of millions of nucleotides, and is most often found paired with a partner strand. These strands wrap around one another in the familiar double helix. The code is quite easy to read: you simply step down the strand of DNA one nucleotide at a time and read off the bases: A, T, C or G. This is exactly what your cells do: they scan down a messenger RNA (copied from the DNA), and use ribosomes to build proteins based on the code that is read. This is also how researchers determine the sequence of a DNA strand: they clip off one nucleotide at a time to see what it is.
Your genetic information, inherited from your parents, is your most precious possession. It guided the construction of your body in the first nine months of your life and it continues to control all of the basic functions of living. Each of your cells is constantly using this information, asking questions about how to control blood sugar levels and body temperature, how to digest different foods and how to deal with new environmental challenges, and thousands of other important questions. The answers are held in the DNA. Hundreds of different proteins are built to interact with this information: to read it and use it to build new proteins, to copy it when the cell divides, to store and protect it when it is not actively being used, and to repair the information when it becomes corrupted by chemicals or radiation.
DNA is arguably one of the most beautiful molecules in living cells. Its graceful helix is pleasing to the eye. DNA is also one of the most familiar molecules, the central icon of molecular biology, easily recognized by everyone. To some, it may carry a negative connotation, being a pervasive symbol for activists against genetically engineered produce. To others, it may bring to mind advances in forensics such as the DNA fingerprinting used in many recent high-profile trials. Some may have seen it in science fiction, modified to build dinosaurs or store cryptic messages from aliens. To all it is a pervasive symbol of our growing understanding of the human body and our close kinship with the rest of the biosphere, and the moral and ethical issues that must be addressed in the face of that knowledge.
DNA is perfect for the storage and readout of information. It is laden with information. Every surface and edge of the molecule carries information. The basic mechanism by which DNA stores and transmits genetic information was discovered in the 1950's by Watson and Crick. This basic information is stored in the way that the bases match one another on opposite sides of the double helix--adenine with thymine, guanine with cytosine--forming a set of complementary hydrogen bonds.
Additional 'extragenetic' information is read from the surfaces that are left exposed in the double helix. In the major groove (the wider of the two grooves in the structure), the different base pairs have a characteristic pattern of chemical groups that carry information. These include hydrogen bond donors and acceptors, as well as a site with a large, bulky group in adenine-thymine base pairs or a small group in guanine-cytosine base pairs. In the minor groove, there is a different arrangement of chemical groups that carry additional information. As revealed in hundreds of structures in the PDB, this extragenetic information is used by proteins to read the genetic code in DNA without unwinding the double helix. It is also targeted by a number of toxins and drugs that attack DNA.
DNA adopts the familiar smooth double helix, termed a B-helix, under the typical conditions found in living cells. An example is shown in the PDB entry 1bna. Under other conditions, however, DNA can form other structures, as revealed in two early crystal structures: PDB entries 1ana and 2dcg. The structure found in PDB entry 1ana, with tipped bases and a deep major groove, is termed A-DNA. It is formed under dehydrating conditions. Also, RNA most often shows this form, because its extra hydroxyl group on the sugar gets in the way, making the B-form unstable (look, for instance, at the A-helical structure of transfer RNA shown in a previous Molecule of the Month). The form found in PDB entry 2dcg, which winds in the opposite direction from A-DNA and B- DNA, is termed Z-DNA. It is found under high salt conditions and requires a special type of base sequence, with many alternating cytosine-guanine and guanine-cytosine base pairs.
We often think of DNA as a perfect, smooth double helix. In reality, DNA has a lot of local structure. The small piece of DNA shown in PDB entry 1bna, shows some of the common variations. At the top, the helix is bent to one side, distorted by the way that the helices are packed into the crystal. At the bottom, two of the bases are strongly propeller twisted--they are not in one perfect plane. This improves the way that the bases stack on top of one another along each strand, stabilizing the whole double helix. As more and more structures of DNA are studied, it is becoming clear that DNA is a dynamic molecule, quite flexible on its own, which is bent, kinked, knotted and unknotted, unwound and rewound by the proteins that interact with it.
To locate DNA structures in the PDB using the SearchFields interface, in the "Contains Chain Type" section select DNA-YES and all others NO. A list of all DNA structures in the PDB as of November, 2001 is available at http://www.rcsb.org/pdb/molecules/pdb23_report.html. For more information on DNA, see http://www.rcsb.org/pdb/molecules/pdb23_5.html.
Glycogen Phosphorylase: Moderation for the Sweet Tooth
Sugar is released from glycogen by the enzyme glycogen phosphorylase. It clips glucose from the chains on the surface of a glycogen granule. The enzyme is a dimer of two identical subunits, which can be seen in PDB entry 6gpb. Two nucleotides, are bound at the entrance to the active site, which is found in a deep cleft. Short chains of sugars similar to the ends of glycogen chains bind into another cleft that the enzyme uses to grip the glycogen granule. In its cleavage reaction, glycogen phosphorylase uses a phosphate molecule, connecting it to the sugar as it is released. A second enzyme, phosphoglucomutase, then shifts the position of the phosphate to a neighboring carbon atom in the sugar, making the sugar ready for breakdown by glycolysis.
As you might imagine, this process is highly regulated. Traffic of sugar into and out of storage in glycogen is used to control the level of glucose in the blood, so glycogen phosphorylase must be activated when sugar is needed and quickly shut down when sugar is plentiful. It is controlled in several ways. First, the enzyme is activated by adding a phosphate molecule to a serine amino acid (serine 14) on the back side of the enzyme. The phosphate causes a large shift in the shape of the enzyme, shifting it into the active conformation. Two special enzymes control the addition and removal of this phosphate, based on levels of the sugar- monitoring hormones insulin and glucagon, and other hormones such as epinephrine (adrenaline).
Also, binding of other molecules can modify the activity of the molecule. For instance, AMP (adenine monophosphate) binds to a different site on the back side of the molecule, causing the same shift to the active conformation. This is useful, because AMP is a product of ATP breakdown and will be more plentiful when energy levels are low and more sugar is needed.
Glycogen phosphorylase is activated by a change of shape. The structure in PDB entry 8gpb is in the inactive T state, and the structure in PDB entry 1gpa is in the active R state. (T stands for tense and R for relaxed, a notation developed when the first allosteric enzymes were being studied, although structures such as these have shown that the idea of tension does not really apply at the molecular level). The shift between the two shapes is controlled by phosphorylation of serine 14 or binding of AMP to the regulatory site. The R-state structure shown here has phosphates attached to the serines and a sulfate group in the site that binds to AMP.
Glycogen is used in many organisms, from humans to yeast. Much of the scientific work on the enzyme has been done with rabbit glycogen phosphorylase, such as those found in PDB entries 8gpb and 1gpa. You can look at the slightly different enzyme from yeast in PDB entry 1ygp. This file contains the two protein chains and several small molecules. One such small molecule is the cofactor pyridoxal phosphate, a reactive molecule which binds tightly in the active site and is used to assist in the reaction. A phosphate is bound in each subunit next to the key threonine amino acid that is used for regulation, controlling an allosteric change similarly to serine 14 in the rabbit form. As you are looking at this enzyme, notice how the two protein chains wrap arms around one another. This allows the subunits to work together when responding to the small changes in shape that are used for control.
A list of all glycogen phosphorylases in the PDB as of December, 2001 is available at http://www.rcsb.org/pdb/molecules/pdb24_report.html. For suggestions for further reading about antibodies, see http://www.rcsb.org/pdb/molecules/pdb24_4.html.