Molecule of the Month: Vancomycin
The antibiotic vancomycin blocks the construction of bacterial cell walls.
Positive and Negative
Exploring the Structure
VanA and D-alanine-D-alanine Ligase (PDB entries 1e4e and 2dln)
We can learn about the evolution of VanA by looking at other bacterial proteins. VanA is a D-alanine-D-lactate ligase, indicating that it adds lactate to the growing peptidoglycan chain. The enzyme that makes the normal peptidoglycan is a D-alanine-D-alanine ligase, which adds alanine to the chain. Comparing the two structures, from PDB entries 1e4e and 2dln , shows that they are quite similar, providing evidence that the enzyme providing resistance evolved from the normal enzyme. To explore these two structures in more detail, click on the image for an interactive JSmol.
Topics for Further Discussion
- You can explore a variety of similar antibiotics and the enzymes involved in synthesizing them by searching for "glycopeptide antibiotics."
- You can look at the VanX protein in PDB entry 1r44, which is also needed for resistance against vancomycin. It is a small enzyme that breaks down any D-alanine-D-alanine peptides that may be present in the cell wall, making room for VanA to build its modified peptides.
December 2015, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2015_12