December 2002 Molecule of the Month by David Goodsell
Keywords: electron carrier activity, electron transport chain, heme binding, respiratory chain, oxidation reduction, cytochrome oxidase, cytochrome bc1
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 here from 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, colored red here. 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. As shown on the next page, the protein also determines where cytochrome c fits into the overall cellular electronic circuit.
A Venerable Family
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.
Cytochrome c forms one connection in a hard-wired cellular electronic circuit. It transfers electrons at the last step in the production of cellular energy. These electrons are originally obtained through the breakdown of sugar, and end up being attached to oxygen to form water (this is the ultimate fate of the oxygen that we breathe). Cytochrome c transfers individual electrons between two large protein complexes, gathering electrons from cytochrome bc1 complex, shown on the left from PDB entry 1kyo, and delivering them to cytochrome oxidase complex, shown on the right from PDB entry 1oco (see also the Molecule of the Month for May 2000). These two complexes perform the heavy work of energy production. As electrons flow through their electron-carrying groups, shown in red, they pump protons across a membrane, shown schematically as the yellow stripe. These protons are then used to power production of ATP. Cytochrome c keeps the entire engine running smoothly, shuttling electrons from one complex to the other as needed.
Exploring the Structure
PDB entry 1kyo gives a close-up view of how electrons are transferred between carriers inside cells. Electrons do not flow through a continuous wire, like in our familiar appliances. Instead, at these small distances electrons tunnel directly from one carrier to the next. This picture shows the complex of cytochrome c (at the top) and the large cytochrome bc1 complex, shown at the bottom. The protein chain in cytochrome c is shown in pink tubes and the protein chains in the bc1 complex are shown in yellow tubes. The hemes are shown with spheres at each atom, with the iron atoms in yellow. Notice how the heme group of cytochrome c is pushed close to a heme group in the bc1 complex. At this distance, electrons tunnel from one heme to the next in less than a millionth of a second.
Information on Cytochrome c
Richard E. Dickerson (1980): Cytochrome c and the Evolution of Energy Metabolism. Scientific American 242 (3), pp. 136-153.
Christian Lange and Carola Hunte (2002): Crystal Structure of the Yeast Cytochrome bc1 Complex with its Bound Substrate Cytochrome c. Proceedings of the National Academy of Science USA 99, pp. 2800-2805.
© 2015 David Goodsell & RCSB Protein Data Bank