Penn researchers determine structure of smallpox virus protein bound to DNA

Structure could aid in anti-viral drug design



Three-dimensional rotation view of the smallpox virus topoisomerase enzyme-DNA complex (DNA, yellow; topoisomerase, blue; covalent bond between the topoisomerase and the DNA, pink sphere)
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(Philadelphia, PA) - Researchers at the University of Pennsylvania School of Medicine have determined the structure of an important smallpox virus enzyme and how it binds to DNA. The enzyme, called a topoisomerase, is an important drug target for coming up with new ways to fight smallpox. The researchers present their findings in the August 4 issue of Molecular Cell.

"This enzyme is one of the most closely studied DNA-modifying enzymes in biology," says Frederic D. Bushman, PhD, Professor of Microbiology, one of the senior authors. "The structure of the DNA complex has been long-awaited." DNA-modifying enzymes bind to specific sequences in the genetic code to aid in the many steps of DNA replication.

The smallpox virus is one of the most easily transmissible infectious diseases known to humans, resulting in up to 30 percent mortality. The efficiency with which it spreads, combined with the deadly nature of the disease, has raised fears that smallpox could be revived for use in bioterrorism. Knowing the exact three-dimensional structure of smallpox virus proteins could help researchers design antiviral agents, but few structures of whole viral proteins exist.

Poxviruses are large viruses that contain two strands of DNA and replicate themselves entirely in the cytoplasm of infected cells. Poxviruses do not take over the genetic machinery inside the nucleus of the host cell, as many viruses do. Because of this strategy, poxviruses encode many of the enzymes they need to replicate their own genes, and hence reproduce. One of these enzymes is a topoisomerase, which is used by the virus to relieve the excessive twisting of DNA strands that normally occurs during DNA replication and transcription of the viral genes. Upon initial infection, the poxviruses come already equipped with some proteins, including topoisomerases, to kick-start replication.

The structure was determined in a collaborative effort between the Bushman lab and the lab of the other senior author Gregory D. Van Duyne, PhD, Professor of Biochemistry and Biophysics and an Investigator with the Howard Hughes Medical Institute (HHMI). Using purified topoisomerase enzyme that had been expressed in bacterial cells, they bound the enzyme to short segments of DNA that contained the viral topoisomerase's specific recognition sequence. They then determined the three-dimensional structure of the topoisomerase-DNA complex using X-ray crystallography.

One of the primary differences between the viral topoisomerase enzyme and the closely related human enzyme that functions in the nucleus of all human cells is that the viral enzyme only relaxes supercoiled DNA when it binds to specific DNA sequences. The structure of the poxvirus topoisomerase-DNA complex provides some important clues about how this recognition and activation mechanism works.

"The more the viral enzyme differs from the human nuclear enzyme, the more likely it is that inhibitors could be developed that are specific to the viral enzymes," says Bushman.

Knowing the three-dimensional structure of the smallpox virus topoisomerase-DNA complex will also facilitate the design of agents to combat poxvirus infections. Topoisomerases are some of the most widely targeted proteins by drugs that are intended to inhibit growth of the cell. Drugs that target topoisomerases generally stabilize an intermediate of the enzyme's reaction in which one of the DNA strands is broken. If these breaks are not repaired, the DNA cannot be replicated and the cell dies.

In the case of smallpox virus, the hope is that drugs targeted to the viral topoisomerase enzyme will prevent viral replication through a similar mechanism. The X-ray structure provides a template for designing small molecules that could stabilize the broken DNA in the intermediate form, thereby killing smallpox virus particles.

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Study co-authors are Kay Perry and Young Hwang, both from Penn. The research was supported by HHMI and the National Institutes of Health through the Middle Atlantic Regional Center of Excellence.

This release and a related image and video can also be seen at: www.uphs.upenn.edu/news.

PENN Medicine is a $2.9 billion enterprise dedicated to the related missions of medical education, biomedical research, and high-quality patient care. PENN Medicine consists of the University of Pennsylvania School of Medicine (founded in 1765 as the nation's first medical school) and the University of Pennsylvania Health System.

Penn's School of Medicine is ranked #2 in the nation for receipt of NIH research funds; and ranked #3 in the nation in U.S. News & World Report's most recent ranking of top research-oriented medical schools. Supporting 1,400 fulltime faculty and 700 students, the School of Medicine is recognized worldwide for its superior education and training of the next generation of physician-scientists and leaders of academic medicine.

The University of Pennsylvania Health System includes three hospitals, all of which have received numerous national patient-care honors (Hospital of the University of Pennsylvania; Pennsylvania Hospital, the nation's first hospital; and Penn Presbyterian Medical Center); a faculty practice plan; a primary-care provider network; two multispecialty satellite facilities; and home care and hospice.


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