Molecule of the Month: Penicillin-binding Proteins

Penicillin attacks the proteins that build bacterial cell walls

D-alanyl-D-alanine peptidase, with a reactive serine amino acid in magenta.
D-alanyl-D-alanine peptidase, with a reactive serine amino acid in magenta.
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Bacteria pose a continual threat of infection, both to humans and to other higher organisms. Thus, when looking for new ways to fight infection, it is often productive to look at how other plants, animals and fungi protect themselves. This is how penicillin was discovered. Through a chance observation in 1928, Alexander Fleming discovered that colonies of Penicillium mold growing in his bacterial cultures were able to stave off infection. With more study, he found that the mold was flooding the culture with a molecule that killed the bacteria, penicillin.

Magic Bullet

Penicillin and other beta-lactam antibiotics (named for an unusual, highly reactive lactam ring) are very efficient and have few side effects (apart from allergic reactions in some people). This is because the penicillin attacks a process that is unique to bacteria and not found in higher organisms. As an additional advantage, the enzymes attacked by penicillin are found on the outside of the cytoplasmic membrane that surrounds the bacterial cell, so the drugs can attack directly without having to cross this strong barrier.

Bursting Bacteria

When treated with low levels of penicillin, bacterial cells change shape and grow into long filaments. As the dosage is increased, the cell surface loses its integrity, as it puffs, swells, and ultimately ruptures. Penicillin attacks enzymes that build a strong network of carbohydrate and protein chains, called peptidoglycan, that braces the outside of bacterial cells. Bacterial cells are under high osmotic pressure; because they are concentrated with proteins, small molecules and ions are on the inside and the environment is dilute on the outside. Without this bracing corset of peptidoglycan, bacterial cells would rapidly burst under the osmotic pressure.

Blocking Construction

Penicillin is chemically similar to the modular pieces that form the peptidoglycan, and when used as a drug, it blocks the enzymes that connect all the pieces together. As a group, these enzymes are called penicillin-binding proteins. Some assemble long chains of sugars with little peptides sticking out in all directions. Others, like the D-alanyl-D-alanine carboxypeptidase/transpeptidase shown here (PDB entry 3pte ), then crosslink these little peptides to form a two-dimensional network that surrounds the cell like a fishing net.

D-alanyl-D-alanine peptidase (left) and beta-lactamase (right).
D-alanyl-D-alanine peptidase (left) and beta-lactamase (right).
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Penicillin Resistance

Of course, bacteria are quick to fight back. Bacteria reproduce very quickly, with dozens of generations every day, so bacterial evolution is very fast. Bacteria have developed many ways to thwart the action of penicillin. Some change the penicillin-binding proteins in subtle ways, so that they still perform their function but do not bind to the drugs. Some develop more effective ways to shield the sensitive enzymes from the drug or methods to pump drugs quickly away from the cell. But the most common method is to create a special enzyme, a beta-lactamase (also called penicillinase) that seeks out the drug and destroys it.

Many beta-lactamases use the same machinery as used by the penicillin-binding proteins--so similar, in fact, than many researchers believe that the beta-lactamases were actually developed by evolutionary modification of penicillin-binding proteins. The penicillin-binding proteins, like the one shown on the left (PDB entry 3pte ), use a serine amino acid in their reaction, colored purple here. The serine forms a covalent bond with a peptidoglycan chain, then releases it as it forms the crosslink with another part of the peptidoglycan network. Penicillin binds to this serine but does not release it, thus permanently blocking the active site. Beta-lactamases, like the one shown on the right (PDB entry 4blm ), have a similar serine in their active site pocket. Penicillin also binds to this serine, but is then released in an inactivated form. Other beta-lactamases do the same thing, but use a zinc ion instead of a serine amino acid to inactivate the penicillin.

Exploring the Structure

The PDB entry 1hvb shows a penicillin-binding protein in action. The enzyme is a D-alanyl-D-alanine carboxypeptidase/transpeptidase that creates a crosslink between two chains in the peptidoglycan net. The structure contains a molecule specially designed by researchers to capture a snapshot of the process of crosslinking. Cephalosporin, a drug similar to penicillin, is bound directly to the serine in the active site. The drug is in the position normally occupied by one of the strands to be crosslinked, as indicated by the transparent dots that extend to the left. A little peptide has been attached to this drug in the position normally occupied by the other strand in the crosslink. This structure shows how the complex might look just after the crosslink is made.

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  1. Kelley, J.A., Kuzin, A.P., Charlier, P. and Fonze, E. (1998) X-ray studies of enzymes that interact with penicillins. Cell and Molecular Life Sciences 54, pp. 353-358.
  2. Waxman, D.J. and Strominger, J.L. (1983) Penicillin-binding proteins and the mechanism of action of beta-lactam antibiotics. Annual Review of Biochemistry 52, pp. 825-869.

May 2002, David Goodsell
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.More