Zuzalysin, an enzyme secreted by the bacterium Porphyromonas gingivalis and associated with periodontal disease, has been the subject of a detailed study revealing its ability to self-organize into increasingly large structures, culminating in a dodecahedral protein cage. This enzyme is the only one larger than 5 MDa deposited in the Protein Data Bank (PDB) with a resolution of 1.8 Å or better.
The research, published in Angewandte Chemie International Edition, details how zuzalysin's organization determines the access of molecules to its active sites. The complex structure, containing 60 active sites, is larger than viruses such as parvovirus or poliovirus. The atomic resolution allows for the observation of molecular details and the analysis of one of the largest enzyme complexes characterized with such precision.
Molecular geometry regulates enzyme activity. Zuzalysin is built from monomers weighing around 95 kDa that associate, promoted by calcium, forming pentamers (0.5 MDa) and larger structures up to the 5.6 MDa dodecahedron. Each form has a different activity depending on the size of its pores, which govern substrate access. The cage has greater proteolytic activity than the bipentamer but lower than the pentamer.
The structure determination was achieved using cryo-electron microscopy (cryo-EM) and X-ray crystallography. Cryo-EM allowed for a three-dimensional reconstruction with a resolution of 1.8 Å. Molecular dynamics simulations were also used to study the protein's flexibility and movements.
The study involved collaboration between teams specializing in structural biology, microbiology, and computing, utilizing European scientific infrastructures such as the ALBA synchrotron in Cerdanyola del Vallès (Catalonia) and the SOLARIS synchrotron in Poland. Understanding zuzalysin expands knowledge of protein function and may contribute to research into bacterial virulence mechanisms and biotechnological applications.
