3D structure and significance of the GΦXXG helix packing motif in tetramers of the E1β subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum

As part Of a Structural genomics project, we have determined the 2.0 Angstrom structure of the E1 beta subunit of pyruvate dehydrogenase from Pyrobaculum aerophilum (PA), a thermophilic archaeon. The overall fold of E1 beta from PA is closely similar to the previously determined E1 beta structures from humans (HU) and P. putida (PP). However, unlike the HU and PP structures, the PA structure was determined in the absence of its partner subunit, E1 alpha. Significant structural rearrangements occur in E1 beta when its E1 alpha partner is absent, including rearrangement of several secondary Structure elements such as helix C. Helix C is buried by E1 alpha in the HU and PP structures, but makes crystal contacts in the PA structure that lead to an apparent beta (4) tetramer. Static light scattering and sedimentation velocity data are consistent with the formation of PA E1 beta tetramers in solution. The interaction or helix C with its symmetry-related counterpart stabilizes the tetrameric interface, where two glycine residues on the same race of one helix create a packing surface for the other helix. This G Phi XXG helix-helix interaction motif has previously been found in interacting transmembrane helices, and is round here at the E1 alpha -E1 beta interface for both the HU and PP alpha (2)beta (2) tetramers. As a case study in structural genomics, this work illustrates that comparative analysis of protein structures can identify the structural significance of a sequence motif.