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Mechanisms of
Bacterial Resistance
to Aminoglycoside Antibiotics

2019 RCSB PDB Video Challenge for High School Students

Learn about the action of aminoglycoside antibiotics and the mechanisms of resistance


Before you begin

In order to comprehend the information on antibiotic action and resistance in this section, you should be familiar with the biomolecular concepts listed below:

I. What are antibiotics?

Antibiotics are small molecules, originally discovered as defensive molecules made by fungi and other organisms, and now created by medical scientists. They bind to essential bacterial molecules, such as enzymes and ribosomes, blocking the growth of the bacteria or killing them. Because these bacterial proteins are structurally different from their animal equivalents or are non-existent in them, they cause no harm to the organism treated for bacterial infection.

Figure 1 presents main classes of antibiotics and their target protein/molecule organized by the biochemical process that they interrupt in bacteria. In this video challenge, we will be focusing only on the action of and resistance to the aminoglycoside class. Last year’s challenge was focused on the beta-lactam class.


Figure 1

Main classes of antibiotics and their target protein/molecule organized by the biochemical process that they interrupt in bacteria. Download as PDF

II. How aminoglycoside antibiotics work

The aminoglycoside antibiotics are made by some bacteria to protect themselves from competing bacteria. They are particularly effective because they are very specific: they attack bacterial ribosomes, corrupting protein synthesis in the bacterium, but they don't attack the ribosomes of many other organisms, including our own ribosomes.

Ribosomes are the molecular machines that build new proteins based on the genetic information carried in the messenger RNA. Ribosomes are made up of multiple protein chains and rRNA that form the small and the large subunits. To learn more about the ribosomal subunits, read the Molecule of the Month on the topic.

Figure 2 shows eukaryotic and bacterial ribosomes drawn to scale and highlights the key differences in the nomenclature of their key components.

Figure 2

Eukaryotic ribosomes; PDB ID 6ek0 and prokaryotic ribosomes; PDB ID 4v5d.

Figure 3

Location of the A, P, and E binding sites inside ribosomes. tRNAs are shown in yellow, the mRNA in red, the beginnings of the polypeptide chain in aqua. PDB ID 4v5d

Despite structural differences, the ribosome in bacteria and prokaryotes follow the same steps in protein synthesis. Once the messenger RNA and a special initiator tRNA (different for prokaryotes and eukaryotes) bind to the smaller subunit of ribosomes, both subunits come together, creating the enzymatic environment for creating new protein chains. The stages of protein synthesis are described in the Molecule of the Month on Ribosome.

The ribosomes have 3 binding sites for the tRNA: A (acceptor site), P (peptidyl site), and E (exit site). Figure 3 shows the locations of these sites inside the ribosomes. The A (acceptor site) site is where the a tRNA carrying a matching codon to mRNA binds. During this step, the ribosome uses several interactions to test this pairing, ensuring that the base pairing is correct. You can explore these interactions in 3D in the Exploring the Structure section, in the Molecule of the Month on Ribosome.

The aminoglycoside antibiotics bind at the A site and they interfere with the recognition of the the matching tRNA, ultimately leading to mistakes in building the new protein chains. You can explore the aminoglycoside binding site in 3D in the Exploring the Structure section of the Molecule of the Month on Aminoglycoside Antibiotics.

Another mode of action for the aminoglycoside antibiotics is binding to the large subunit of the ribosome and causing problems at the end of protein synthesis, blocking the recycling of ribosomes after they are finished making a protein. You can explore this process in the Structural Biology Highliglights article Antibiotics and Ribosome Function.

Aminoglycoside antibiotics are used mainly to treat infections caused by gram-negative bacteria in a clinical setting.

Table 1: Examples of Aminoglycoside Antibiotics and PDB structures with the antibiotic bound


III. Mechanisms of bacterial resistance to aminoglycoside antibiotics

In the face of overuse and misuse of antibiotics, new strains of bacteria have emerged that can proliferate even in the presence of the newest antibiotics. There are multiple ways the bacteria adapt to develop resistance against the aminoglycoside antibiotics. Of current clinical prominence are the following three molecular mechanisms:

  1. Aminoglycoside modifying enzymes
  2. Ribosomal methyltransferases
  3. Efflux pumps that remove the antibiotics from the bacterial cell

There are two ways in which the resistance genes for each of these mechanisms can be passed on: via Chromosome, where the gene is transferred from generation to generation (vertical transfer) and via a plasmid that can be passed from bacterial species to species (horizontal transfer).

1. Aminoglycoside modifying enzymes

Aminoglycoside modifying enzymes alter the structure of antibiotics directly so that they can’t attach to their target. They are a large family containing three subclasses based on the type of modification that they apply to the the antibiotic:

O-nucleotidyltransferase (ANT):
these enzymes add a nucleotide to the drug

Before Reaction: Tobramycin: TOY

After Reaction: Adenylated Tobramycin 51H


N-acetyltransferases (AAC):
these enzymes add an acetyl group to the antibiotic

Before Reaction: Gentamycin: LLL

After Reaction Acetylated Gentamicin 8MM


O-phosphotransferase (APH):
these enzymes connect a phosphate to the drug

Table 2: Example PDB entries for aminoglycoside modifying enzymes

2. Ribosomal methytransferases

The ribosomal methytransferases modify ribosomes enzymatically by adding methyl groups to a nucleotide on the 16S rRNA in the aminoglycoside binding site. This does not affect the function of the ribosome, but prevents the antibiotic from binding.

Table 3: Example PDB structures for ribosomal methytransferases

3. Efflux pumps that remove the antibiotics from the bacterial cell

Multidrug resistance transporters or efflux pumps find drugs that try to gain entry through a cell membrane and they transport them back outside.

Bacteria possess multidrug resistance (MDR) gene regulators that can sense when the antibiotics get into the bacterial cell, and prompt the synthesis of the multidrug resistance pumps to eject them.

Table 4: Example of efflux pump and a multidrug resistance (MDR) gene regulator

Visualization Resources

  1. The user guide for NGL can be found here. The NGL is the default 3D viewer accessible from each structure summary page, from the tab “3D View”.



  1. Sylvie Garneau-Tsodikovaa and Kristin J. Labby (2016) Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives. Medchemcomm. 7(1): 11–27.