Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori

Half the world's population is chronically infected with Helicobacter pylori(1), causing gastritis, ulcers and increased incidence of gastric adenocarcinoma(2). Its proton-gated inner-membrane urea channel, HpUreI, is essential for survival in the acidic environment of the stomach(3). The channel is closed at neutral pH and opens at acidic pH to allow rapid urea access to cytoplasmic urease(4). Urease produces NH(3) and CO(2) that neutralize entering protons and thus buffer the periplasm to pH ∼6.1 even in gastric juice at pH <2.0. Here we report the structure of HpUreI, revealing six protomers assembled in a hexameric ring surrounding a central bilayer plug of ordered lipids. Each protomer encloses a channel formed by a twisted bundle of six transmembrane helices. The bundle defines a novel fold comprising a two-helix hairpin motif repeated three times around the central axis of the channel, without the inverted repeat of mammalian urea transporters. Both the channel and the protomer interface contain residues conserved in the AmiS/UreI superfamily, suggesting preservation of channel architecture and oligomeric state in this superfamily. Predominantly aromatic or aliphatic side chains line the entire channel and define two consecutive constriction sites in the middle of the channel. Mutation of Trp153 in the cytoplasmic constriction site to Ala or Phe reduces the selectivity for urea compared to thiourea, suggesting that solute interaction with Trp153 contributes specificity. The novel hexameric channel structure described here provides a new paradigm for permeation of urea and other small amide solutes in prokaryotes and archaea.