BOSTON--A team of Harvard Medical School researchers have established the 3-D, atom-by-atom structure of a DNA-replicating enzyme at work. This protein, called T7 DNA polymerase, is used in scientific laboratories throughout the world to sequence DNA. This structure will be of special interest to researchers who develop drugs targeting DNA replication. Many antiviral drugs, including the AIDS drug AZT and drugs against herpes simplex virus, inhibit DNA polymerase. In addition, this work may guide the development of better reagents for DNA sequencing--highly sought-after products in this age of the Human Genome Project.
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This is the largest protein complex ever to be revealed by the leading method--called MAD--of obtaining high resolution images in X ray crystallography. The structure will be published in the January 15 Nature, along with results from a research collaboration led by crystallographer Thomas Ellenberger and biochemist Charles Richardson, assistant professor and professor, respectively, of biological chemistry and molecular pharmacology at Harvard Medical School.
Other researchers had previously figured out the crystal structure of related enzymes but had never been able to include all the players necessary for DNA duplication. By contrast, this work captures a snapshot of replication at work: the structure shows the polymerase (green, blue, red, salmon-colored areas) bound intimately to a twisted DNA double helix (pink and yellow areas). Where the double helix ends, the DNA continues as a short, single-stranded stretch (yellow), and this is where the polymerase was just about to attach another DNA building block (arrow), when it was frozen in action by the crystallization process.
Moreover, this work for the first time depicts a so-called replicative polymerase. Various types of DNA polymerases occur in every cell of every living thing, but the enzymes crystallized in earlier studies function more like repair enzymes that fill in small nicks in the DNA. They are slow and make errors frequently. This structure, however, shows a polymerase that zips along the DNA during cell division and faithfully replicates the entire chromosome at a rate of up to 400 building blocks--or nucleotides--per second. To do that, it needs the help of a second protein (shown in orange) to stay clamped to the DNA.
This work shows in exquisite detail how the polymerase recognizes the right nucleotide to be paired to the single-stranded DNA, and thus helps explain how this enzyme achieves its high accuracy of about one mistake per million nucleotides. Mistakes cause mutations and, in certain genes, can lead to cancer.
Editors: A more detailed version of this story is available on request. The other researchers on this project include lecturer Stanley Tabor, who figured out the biochemical conditions to enable crystallography, postdoctoral fellow Sylvie Doublié, who produced the crystal structure, and Alexander Long, a technician.
Journal
Nature