Beta-barrel transmembrane proteins are found only in the outer membranes of Gram-negative bacteria and the eukaryotic organelles of bacterial origin, mitochondria and chloroplasts. These proteins are assembled in the membrane by a machine whose central component is a highly conserved protein; in Escherichia coli, this protein is known as YaeT. The multi-protein machine is believed to mediate the targeting, folding and insertion of other beta-barrel proteins, but the molecular mechanisms by which it performs these functions are unknown. In order to improve our understanding of these processes, structural information about the YaeT complex was obtained using biochemical and crystallographic tools.

YaeT is the only beta-barrel transmembrane protein among the five members of the protein complex. It also has one or more polypeptide transport associated (POTRA) domains in the periplasm, which are implicated in substrate protein recognition. The crystal structure of the periplasmic domain of YaeT presented here reveals the POTRA fold and a region that is important for the formation of a crystallographic dimer. This dimeric interface demonstrates one way for POTRA domains to mediate protein-protein interactions and suggests a possible mode of interaction of POTRA domains with substrate proteins. The biochemical isolation and characterization described here reveals that the YaeT complex exists in a stable form in detergent solution, in which YaeT is monomeric. Analysis of the protein-protein interactions in the complex leads to a model of the organization of the five component proteins. The interactions suggest that there are two spatially distinct regions of the complex in the periplasm. Overall, this work provides more structural information about the YaeT complex and lays the foundation for future investigations to understand OMP biogenesis.