Bringing Structure to Biology
Our calendar image for August focuses not on a protein, but on one of the thousands of small molecules in the Protein Data Bank. This particular molecule is vital in our continuing fight against infection and has a long forgotten history.
The year is 350 AD. In a village in Nubia, which will become northern Sudan, a family sits down to drink some beer with their meal. During the fermentation process Streptomyces bacteria in the brew produce significant amounts of the antibiotic tetracycline. Fortuitously, humans deposit tetracycline in their bones, enabling archaeologists to discover it when examining the mummified remains of these people some 1600 years later.
The discovery of an antibiotic in humans long before its modern-day usage (it was patented in 1953) came as something of a surprise, but whether this ancient antibiotic production and usage was intentional is impossible to know. It would, however, have done the same job then, as now. Streptomyces bacteria make tetracycline for chemical warfare- it kills other bacteria which are competing with them for nutrients.
A small spanner in a big machine
Tetracycline (shown above) is a small molecule. It has 32 atoms (not counting hydrogens) arranged, as the name implies, into four rings. It acts by stopping a huge molecular machine of around 150 thousand atoms- the ribosome. It binds to the ribosome, the complex which makes new proteins, and blocks the binding of transfer RNA. Transfer RNA brings in amino acids, the building blocks of proteins to be added to the protein being made. Just as if a cargo ship can’t dock, the cargo can’t be offloaded, if transfer RNA can’t bind to the ribosome, a new protein can’t be produced.
Our first molecular view of this blockage came in 2001 with the X-ray structure of the smaller subunit of the ribosome (PDB entry 1hnw) with tetracycline bound. Since then several structures of the whole ribosome have been solved, giving more insight into how tetracycline works, for instance PDB entry 4v9a, on which the schematic below is based.
Tetracycline (yellow hexagons) binds to the small subunit of the ribosome. Transfer RNA then cannot dock to bring in a new amino acid (green circles) to add to the growing chain already present attached to the other transfer RNA bound to the ribosome at a second site.
Fighting back- evict the spanner!
Not all bacteria are susceptible to tetracycline. In interspecies bacterial warfare the opposing side has defences, which means that antibiotic resistance is a growing problem. Resistant bacteria prevent tetracycline from blocking their ribosomes primarily by actively pumping it out of the cell. Because the pumping machinery is expensive to produce, and also tends to pump out useful molecules, the pump only manufactured when there’s a need. That means, of course, that a bacterium has to sense when it’s under attack from tetracycline and activate its defences.
This sensing mechanism comes in the form of a protein called TetR (for tetracycline resistance). TetR sits on the DNA which encodes the resistance pump mechanism (eg PDB entry 1qpi) and stops it being activated. When tetracycline enters the cell, it binds to TetR and causes it to change shape slightly (eg PDB entry 2vke), and to fall off the DNA. This DNA is now free to produce the pumping machinery, saving the attacked bacterium from death.
Binding of tetracycline (yellow spheres) causes TetR to change shape slightly from the green cartoon configuration which binds DNA (pink spheres) to the cyan configuration, which does not.
Whether by accident or design, our Nubian family were ingesting relatively high levels of tetracycline many hundreds of years before the antibiotic era. It must have had an effect on the bacteria they shared their environment with, and inevitably would have caused some resistance. Modern-day humans need to be very careful of their antibiotic usage to avoid us entering the post-antibiotic era.
About the artwork
The image from PDBe’s calendar is by Eloise Culshaw from Impington Village College using the batik technique. It shows a bacterium, and overlaid within it tetracycline as displayed in UCSF Chimera.