featured system May 2009
Bacterial Leucine Transporter, LeuT
Many antidepressant drugs, as well as drugs of abuse such as cocaine, block the traffic of neurotransmitters across the cell membrane of nerve axons and glial cells. They bind to a specific transport protein that clears the synapse after a nerve signal, transporting neurotransmitters back into the axon and making it ready for another signal. Researchers at NYCOMPS have made the first steps towards understanding this transporter at the atomic level, by looking to bacteria for help.
The transporter in our nerve cells has proven difficult to purify and crystallize, but a homologous bacterial transporter, LeuT, has been more cooperative. Like the transporter in our nerves, it has a bundle of twelve alpha helices that form a transport channel through the membrane. LeuT is more compact than our transporter, however, and is missing several extensions at the ends of the chain that interact with proteins in the nerve cell. The transport function is similar, though, and is even inhibited by compounds like antidepressants that block transport of neurotransmitters. So, the bacterial protein is providing a powerful model for studying the atomic details of the nerve protein.
LeuT is one of dozens of transporters that shuttle amino acids in and out of bacterial cells. LeuT specializes in small hydrophobic amino acids like leucine and alanine. The transport is powered by the gradient of sodium ions that is normally maintained by healthy cells across their membranes. LeuT acts as a symporter, which links the passage of a sodium ion across the membrane with the transport of the amino acid in the same direction.
Looking at LeuT
The crystal structures solved by NYCOMPS and other researchers, included in PDB entries 2q6h, 2q72, 2qb4, 2qei, and 2qju, capture LeuT frozen by the antidepressant in the middle of performing its job. An amino acid (shown in yellow) is bound deep inside the protein, held by two sodium ions (shown in green). The protein recognizes all aspects of the amino acid, forming specific interactions with both the amino group and the acid group, and forming a hydrophobic pocket perfectly fitted to the small hydrophobic sidechain.
The protein is thought to act like a rocker switch. It starts with an opening towards the outside of the cell. Leucine and sodium enter and bind, then the protein shifts to open inside the cell, releasing the amino acid and sodium. The Jmol image below highlights two sets of alpha helices that are thought to perform the rocking action. The antidepressant molecule binds in the large cavity at the outer entrance to the protein, not directly blocking the binding site for amino acids, but presumably blocking the motion of the protein that is necessary for transport. There is some evidence, however, that antidepressants may bind a bit deeper in the opening of neurotransmitter transporters, so the LeuT structures are only the first installment in this fascinating story.
Click on the JSmol tab for an interactive Jmol.
Lysostaphin (PDB entry 2gu1)
The active site of cholera lysostaphin is very similar to other lysostaphins, such as the autolytic LytM protein from Staphylococcus aureus, with a zinc ion (magenta sphere) coordinated by two conserved histidine amino acids and an aspartate. A water molecule (turquoise sphere) is bound to the zinc and is thought to be important in the cleavage reaction. Lysostaphin also includes two other domains, colored turquoise and blue here, which you can see using the zoom button below. The functions of t
S. K. Singh, A. Yamashita and E. Gouaux (2007) Antidepressant binding site in a bacterial homologue of neurotransmitter transporters.
S. K. Singh (2008) LeuT. Channels 2, 380-389.
Z. Zhou, J. Zhen, N. K. Karpowich, R. M. Goetz, C. J. Law, M. E. A. Reith and D.-N. Wang (2007) LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake. Science 317, 1390-1393.