PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
Header Icons
E-Collection

Related Theme

Surviving in an acid environment

PSI-SGKB [doi:10.1038/fa_psisgkb.2009.34]
Featured Article - August 2009
Short description: The Escherichia coli O157:H7 amino acid antiporter structure reveals clues to how this bacterium survives in the harsh stomach environment.Science 324, 1565-1568 (2009)

Escherichia coli O157 colonies. Source: Centers for Disease Control and Prevention.

Escherichia coli O157:H7 is a virulent strain that can cause severe stomach cramps, diarrhea and vomiting. Although most people recover within a short time, some cases are life-threatening.

E. coli O157:H7 is particularly effective because can survive in the acidic environment of the stomach, where the pH is between 2 and 3. It achieves this by using acid-resistance systems, termed AR2 and AR3, that exchange one substrate for another. In the case of AR2, transport of glutamate is linked to that of agmatine (Agm, the decarboxylated form of arginine) through the antiporter AdiC. This process results in a net expulsion of one proton for each transport cycle.

A previous low-resolution electron crystallographic study of AdiC provided a broad outline of the antiporter structure but could not elucidate the details of mechanism. Now, Gao et al. reveal the X-ray crystallographic structure of AdiC to a resolution of 3.6 Å. Overall, the structure is similar to that of the sodium-coupled symporters such as LeuT, with each molecule of AdiC having 12 transmembrane segments arranged in two layers. The inner layer is surrounded by the outer layer.

When Gao et al. compared the amino-acid sequence of AdiC with those of other related antiporters they found that a third of the conserved residues are in the central cavity, suggesting that it is a substrate-binding site. Of particular note were the four polar or charged residues located at the bottom of the cavity: Asn22, Tyr93, Glu208 and another tyrosine, Tyr365. By mutating these residues the team confirmed that these four are crucial for substrate binding.

Using this information they propose a four-step model to explain how this antiporter works. They suggest that the structure they have solved is of the initial state with the antiporter in an open, outward-facing conformation. The first step is for Arg to bind within the cavity, away from the periplasm. The second is a change in the antiporter to an open conformation, in which Arg is competitively displaced by Agm, the secondary substrate. For the third step, the antiporter bound to Agm closes, removing Agm from the cytoplasm. For the final step, the antiporter opens up to the periplasm to release Agm.

The key residue appears to be Glu208, which is most probably the pH sensor. In the stomach, at pH 2, Glu is mainly protonated and thus attracts the mainly deprotonated substrate amino acids. Once the antiporter changes conformation, Glu faces the intracellular environment, where Glu is deprotonated to produce a binding cavity with a net negative charge that favors the Agm binding.

Although the overall structure of sodium-coupled symporters and AdiC are similar, the newly revealed structure shows that AdiC and the symporters bind substrates differently.

Maria Hodges

References

  1. X. Gao et al. Structure and mechanism of an amino acid antiporter.
    Science 324, 1565-1568 (2009), doi: 10.1126/science.1173654.

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health