Crystal structure and mutational analysis of the Escherichia coli putrescine receptor -: Structural basis for substrate specificity

PotF protein is a periplasmic substrate-binding protein of the putrescine transport system in Escherichia coli. We hare determined the crystal structure of PotF protein in complex with the substrate at 2.3-Angstrom resolution, The PotF molecule has dimensions of 54 x 42 x 30 A and consists of two similar globular domains. The PotF structure is reminiscent of other periplasmic receptors with a highest structural homology to another polyamine-binding protein, PotD. Putrescine is tightly bound in the deep cleft between the two domains of PotF through 12 hydrogen bonds and 36 van der Waals interactions. The comparison of the PotF structure with that of PotD provides the insight into the differences in the specificity between the two proteins. The PotF structure, in combination with the mutational analysis, revealed the residues crucial for putrescine binding (Trp-37, Ser-85, Glu-185, Trp-244, Asp-247, and Asp-278) and the importance of water molecules for putrescine recognition.