2.A.33 The NhaA Na⁺:H⁺Antiporter (NhaA) Family

NhaA homologues have been sequenced from numerous bacteria and archaea. Many prokaryotes possess multiple paralogues. These proteins are of 300-700 amino acyl residues in length. The E. coli protein probably functions in the regulation of the internal pH when the external pH is alkaline, and the protein effectively functions as a pH sensor (Gerchman et al., 1993). It also uses the H⁺ gradient to expel Na⁺ from the cell. Its activity is highly pH dependent. Only the E. coli protein is functionally and structurally well characterized (Padan et al., 2001; Hunte et al., 2005). Its structure reveals a homeodimer, each subunit consisting of a bundle of 12 tilted transmembrane α-helices (Williams et al., 1999; Williams, 2000; Hunte et al., 2006; Olkhova et al., 2006; Screpanti et al., 2006).

Molecular dynamics simulations of NhaA enabled proposal of an atomically detailed model of antiporter function Arkin et al., 2007). Three conserved aspartates are key to this proposed mechanism: Asp¹⁶⁴ (D164) is the Na⁺-binding site, D163 controls the alternating accessibility of this binding site to the cytoplasm or periplasm, and D133 is crucial for pH regulation. Consistent with experimental stoichiometry, two protons are required to transport a single Na⁺ ion: D163 protonates to reveal the Na⁺-binding site to the periplasm, and subsequent protonation of D164 releases Na⁺ (Arkin et al., 2007; Padan, 2008). A Trp at position 136 specifically monitors a pH-induced conformational change that activates NhaA, wheras a Trp at position 339 senses a ligand-induced conformational change that does not occur until NhaA is activated at alkaline pH (Kozachkov and Padan, 2011).The primary function of Li⁺ riboswitches and associated NhaA transporters is to prevent Li⁺ toxicity, particularly when bacteria are living at high pH (White et al. 2022).

Na⁺-H⁺ antiporters are integral membrane proteins that exchange Na⁺ for H⁺ across the cytoplasmic membrane and many intracellular membranes. They are essential for Na⁺, pH, and volume homeostasis, which are processes crucial for cell viability. Accordingly, antiporters are important drug targets in humans and underlie salt resistance in plants. Many Na⁺-H⁺ antiporters are tightly regulated by pH. E. coli NhaA, a prototype pH-regulated antiporter, exchanges 2H⁺ for 1Na⁺ (or Li⁺). The NhaA crystal structure has provided insight into the pH-regulated mechanism of antiporter action and revealed transmembrane segments, which are interrupted by extended mid-membrane chains that have since been found with variations in other ion-transport proteins. This novel structural fold creates a delicately balance electrostatic environment in the middle of the membrane, which might be essential for ion binding and translocation.

The generalized transport reaction catalyzed by NhaA is:

Na⁺ (in) + 2H⁺ (out) ⇌ Na⁺ (out) + 2H⁺ (in)