Phaseolus Vulgaris: Crystal Structure Analysis

The availability of the crystal structure of the potassium dependent asparaginase from Phaseolus vulgaris (PvAspG1) provided insight into the mechanism of potassium activation (Bejger et al., 2014). There are two alkali metal binding sites in each α subunit, located in highly characteristic metal coordination loops. One of them is structural and is referred to as the stabilization loop. It is also present, as a sodium binding loop, in the crystal structure of K+ independent asparaginase from Lupinus luteus (Michalska, Bujacz, & Jaskolski, 2006). The second site is referred to as the activation loop and it is unique to K+ dependent asparaginases. The activation loop of PvAspG1 is formed by eight residues, Val-111, Met-112, Asp-113, Lys-114, …show more content…
Sodium binding results in a conformational change of the activation loop which affects the position of the side chains of three key residues: His-117, which is part of the activation loop in subunit α, and Arg-224 and Glu-250 present in the β-subunit of the other heterodimer. When potassium is present in the activation loop, the side chain of Arg-224 holds the L-aspartate/L-asparagine product/substrate in place in the active site through a fork of hydrogen bonds in a salt bridge between the N atoms of the Arg-224 guanidium group and the α-carboxylate group of the ligand. Glu-250 stabilizes this conformation of the active site by forming hydrogen bonds with the side chains of Arg-224 and His-117. Binding of sodium into the activation loop results in a conformational change whereby the side chain of His-117 swings deeper into the protein core, pushing Arg-224 to rotate away from the active site. The side chain of Glu-250 also moves away from the active site, no longer interacting with the other two residues. It was suggested in the above study, that it is Ser-118 that is responsible for the alkali metal coordination in the activation loop, and ultimately for the operation of the catalytic switch (Bejger et al.,