'Snap shot' captures key cancer-search and destroy enzyme

December 14, 1999

A collaboration between the National Institute of Environmental Health Sciences and the State University of New York at Stony Brook has produced a highly detailed image of a newly discovered class of proteins that searches genetic material for damage from environmental chemicals and sunlight.

The proteins' search for damage to our human cells initiates repairs crucial to preventing such damage from developing into important human diseases, such as cancer.

The work, reported in the Dec. 15 issue of Journal of the European Molecular Biology Organization, opens a window on how DNA repair proteins recognize good DNA from bad DNA. The senior authors are Caroline Kisker, Ph.D., of SUNY and Bennett Van Houten, Ph.D., of NIEHS. Others carrying out the work were Karsten Theis, Ph.D., and Paul J. Chen of SUNY and Milan Skorvaga, Ph.D., of NIEHS.

Using crystallography B the scientists created a detailed image of the atomic structure of the protein, called UvrB. This image of the structure suggests its function, much in the same way a freeze-frame picture of an animal in motion suggests a particular activity such as prey or predator.

UvrB (Uvr stands for the fact that bacteria lacking this enzyme, or protein, are sensitive to killing by UV light) works in conjunction with another protein UvrA to bind and mark the lesion, or damage, caused by the environmental chemical or other environmental factor. When bound to the DNA UvrB marks the site for repair by recruiting UvrC, a molecular scissors, which cuts the damaged site out. All these proteins occur in bacteria, where they can be more readily studied, but the findings should lead to advances in human disease, the scientists said.

For example, the scientists said they can now manipulate the protein molecule, deleting a critical structure, for example, or replacing amino acids, the molecular building blocks of proteins. This 'Lego' approach can be done in 3-D models of the molecule and then, via DNA manipulation, in the actual protein to get a complete picture of how the protein does its job.

Now that they have found and imaged the molecule, Dr. Van Houten said the team now "seeks to understand how the protein helps the body's cells know a piece of damaged DNA from a good piece -- which is comparable to looking through 4 billion Lego blocks in search of one or two defective blocks."

But while a damaged Lego might make a child cry, Dr. Van Houten says, "The defective 'block' in this case -- the defective DNA -- can lead to mutations or cancer. "

The job of search and quality control that UvrB plays inside the cell -- sorting through millions of bases of DNA looking for those bases suffering from environmental damage is crucial. A simple 30 minute walk on the beach can cause a 100,000 of these sunlight induced damages in the skin. Sadly there are people born without these types of repair proteins. They suffer a disease called xeroderma pigmentosum and have a 4000-fold increase in getting skin cancer usually before seeing the eighth birthday.

The structure of the protein was simultaneously discovered by Nobel Laureate Johann Deisenhofer at Southwestern Medical Center in Dallas who first published the structure but without as much detail as the present structure from the Kisker and Van Houten collaboration.

An inability to remove environmentally-induced DNA damage is highly correlated to cancer. For example, defects in human cells are associated with xeroderma pigmentosum, a severe sun sensitivity with a 4000-fold increase in skin cancer B with the cases commonly occurring by age 8. Severe forms of this disease are associated with neurological defects. In skin cancer, which is the most common form of cancer, the scientists said many cases are very likely to be caused by alterations, or polymorphisms, in genes encoding DNA repair enzymes.
-end-
Image available at: http://www.niehs.nih.gov/oc/news/crystal/home.htm

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Background: UvrB is a bacterial protein which functions in nucleotide excision repair and has parallels, or homologs, in human cells. Nucleotide excision repair removes bulky-type lesions in the DNA resulting from sunlight or environmental carcinogens like polycyclic aromatic hydrocarbons; the natural substance, aflatoxin, found in moldy grains, and N-acetylaminofluorene.

Nucleotide excision repair is mediated by a large protein machine which scans the genetic material searching for damage. Once a series of proteins have found and marked the damage site, molecular scissors, called endonucleases, are recruited to remove the strand of DNA containing the damage. Thirty proteins may be involved in this process in human cells.

There are two other major types of repair:

  1. Base excision repair - which removes simple base damage like methylated or oxidize bases and

  2. Mismatch repair - which removes incorrectly paired bases.

The three pathways exist in all bacteria cells and in the cells of higher plants, humans and other animals, fungi, protozoa and algae. Illustrations available:

Slide 1 is the crystal structure of UvrB. The different colors show different domains. UvrB is folded like a large family of proteins called helicases which work to open up the two strands of DNA. The blue beta-hairpin suggested a site for DNA binding. When the structure of UvrB was compared to other helicases that had been crystalized with DNA we found that the DNA tracks close to the beta-hairpin (slide 2). The final slide shows how we believe the DNA tracks along the surface of the protein.

NIH/National Institute of Environmental Health Sciences

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