By solving the 3-D structure of one particular enzyme that controls genes, researchers at Johns Hopkins, working with colleagues at University of Pennsylvania and the Wistar Institute, have discovered how the enzyme adds chemical groups to chromosomes to alter gene function. The research team reports in this week’s Nature that the new structure paves the way for developing new chemical inhibitors and therapies for diseases like cancer.
“We’ve had a chemical inhibitor of p300 for about nine years now, but without the structure, we had no idea how it was working or, more importantly, how to improve on it,” says Philip Cole, M.D., Ph.D., professor and director of pharmacology and molecular sciences at Johns Hopkins.
The enzyme p300/CBP adds chemical acetyl groups to chromosomes, which generally turns genes on. “Some cancers like melanoma appear to be driven by acetylation,” says Cole. Inhibiting such enzymes might be useful anticancer therapies and for other diseases such as diabetes and heart disease.
To figure out the structure of p300/CBP, the researchers overcame obstacles using a number of technical tricks developed over seven years to crystallize the enzyme in the presence of a chemical known to inhibit its activity. The team then used X-rays to determine the structure of the purified protein-inhibitor crystals. Using computers, they then assembled a 3-D model of p300/CBP.
p300/CPB is one of several enzymes - histone acetyltransferases, or HATs - that can put acetyl groups onto chromosomes. But the other enzymes don’t share similar building block patterns with p300/CBP, according to Cole. However, once they had the structure, they were able to compare it with other enzymes and found that the central region of the enzyme, the part that holds the acetyl, has a similar shape as other HATs.
The structure also revealed that p300/CBP puts acetyl groups onto chromosomes by a so-called hit-and-run mechanism. Whereas other enzymes hold onto both the acetyl and the chromosome at the same time and encourage the chemical transfer, p300/CBP holds onto the acetyl and transfers the acetyl to the chromosome without lingering or hanging on.
“The structure shows that p300 has a tunnel that allows the chromosome to bang into it and leave,” says Cole.
The team plans to follow up with enzyme studies to try to develop improved chemical inhibitors for p300/CBP. “We’re still in our infancy of understanding how to go after cancer,” says Cole. “But this definitely is a step in the right direction.”
"This work nicely illustrates the power of enzymology and structural biology to reveal how an important cellular process works," said Warren Jones, Ph.D., Chief of the Biochemistry and Biorelated Chemistry Branch at NIGMS. "This research provides a firm basis for developing drugs to treat diseases, such as certain cancers, associated with unchecked HAT activity."
The research was funded by the National Institutes of Health, FAMRI, the Kaufman Foundation and the Keck Foundation.
Authors on the paper are Ling Wang, Paul Thompson, Yousang Hwang and Cole of Hopkins, and Xin Liu, Kehao Zhao and Ronen Marmorstein of The Wistar Institute in Philadelphia.