Molecular analysis of 3D domain swapping in the acylphosphatase from Escherichia coli

Three-dimensional domain swapping is a mechanism by which proteins form oligomers. At present, the molecular basis that dictates whether some proteins fold in their monomeric form or as intertwined oligomers is poorly understood. Previously, we have described the first intertwined dimer of an acylphosphatase (AcP) from crystals belonging to the orthorhombic space group C222. In this work, we present the first crystallographic structure of monomeric AcP from Escherichia coli (EcoAcP) and compare it with the intertwined structure of the orthorhombic polymorph and a new intertwined dimer structure obtained from crystals belonging to the hexagonal space group P6₁22. The monomeric form contains two molecules in the asymmetric unit, each exhibiting some differences. One of the molecules shows a sodium cation that introduces conformational changes in loop L4 (connecting α2 and β4). This loop is located adjacent to the active site, which is formed by a cleft between loops L1 (connecting β1 and α1) and L3 (connecting β2 and β3), in which phosphate anions have been modelled. Besides, in the monomeric form, the active-site Arg20 forms a salt bridge with the carboxyl-terminal group. This interaction is absent in the intertwined dimer, where the interchange of the terminal β-strand β5 is facilitated by loop L5 (connecting β4 and β5) that serves as a hinge loop. The first residue of this loop, Pro79, has been modelled in a cis conformation in the intertwined structures, whereas it is in a trans conformation in the monomeric form. The low rate of cis-trans proline isomerization would favour the formation of the domain-swapped structure under appropriate conditions. Comparative analysis of the monomer and intertwined dimer structures would facilitate understanding of the molecular basis of oligomer formation.