Lysozyme

First X-ray crystal structure of an enzyme helped scientists understand how proteins carry out reactions

# of atoms:
~1,950

On Nov. 5, 1965, about five months after publishing the first-ever X-ray crystal structure of an enzyme in the journal Nature, David C. Phillips gave a public lecture recounting the feat.

The audience, out for some Friday night entertainment, marveled over the molecular models Phillips had brought with him to the lecture theater at London’s Royal Institution. Hanging from the ceiling was a 32-foot-long string of the enzyme’s 129 amino acids. And on the counter next to Phillips was the same string, only folded into a globular shape a few feet across. The folding, Phillips explained, locked the amino acids together in a way that gave the enzyme its catalytic activity.

“It must have been one of ‘the’ moments in time for a scientist,” says the University of British Columbia’s Stephen G. Withers of the historic lecture. “As a longtime enzymologist, I can only imagine what it was like for Phillips and his colleagues to see inside one of these beasts for the first time ever.”

The enzyme whose anatomy the researchers laid bare—lysozyme—was long known to kill bacteria by chewing through peptidoglycans that strengthen the microbes’ outer cell walls. Alexander Fleming, who would go on to discover penicillin, had identified lysozyme in 1922, after he splashed some drops of nasal mucus onto a plate of bacteria and noticed the organisms stop growing. Lysozyme, scientists would later learn, exists inside the body as a natural defender against bacterial invaders.

Phillips unveils the molecular model of lysozyme (on table in front of him) to the public during a historic lecture at the Royal Institution in 1965. The enzyme’s linear sequence hangs from the ceiling.

Phillips unveils the molecular model of lysozyme (on table in front of him) to the public during a historic lecture at the Royal Institution in 1965. The enzyme’s linear sequence hangs from the ceiling.
Royal Institution Archives

But it wasn’t understood how the enzyme accomplished this task until Phillips and his team determined their 2-Å-resolution X-ray structure of lysozyme from chicken egg whites (Nature 1965, DOI: 10.1038/206757a0). At the time, this version of lysozyme was easier to isolate than human lysozyme.

The 3-D structure revealed lysozyme’s active site, a cleft in the enzyme’s globular landscape where bacterial peptidoglycans fit snuggly and had their glycosidic bonds cleaved. After Phillips’s graduate student at the Royal Institution, Louise N. Johnson, succeeded in crystallizing lysozyme with some amino-sugar units of peptidoglycan chains, the team proposed a mechanism of action for the enzyme.

According to Withers, who refined that mechanism years later (Nature 2001, DOI: 10.1038/35090602), “They did a remarkably good job of fitting everything together,” given that X-ray structures were all calculated by hand back then.

At the time, “a lot was known about how reactions were catalyzed in solution,” Withers continues. The lysozyme structure, he adds, helped scientists understand how those same types of reactions were carried out inside enzymes.

Today, crystallographers routinely use lysozyme to calibrate X-ray instruments, and professors use it to train future generations of structural chemists and biologists.—Lauren Wolf

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