Conformational changes and domain motion of active site loops of apo and holo forms of serine hydroxymethyltransferase enzyme in aqueous medium

Abstract

We have studied conformational changes in a pyridoxal \(5^\prime\)-phosphate (PLP) dependent enzyme, namely serine hydroxymethyltransferase (SHMT), which plays an essential role in catalyzing the reversible simultaneous conversion of L-serine to glycine and tetrahydrofolate (THF) to 5,10-methylenetetrahydrofolate (folinic acid). When the substrate and PLP bind to SHMT, it undergoes a conformational change, transitioning from an open to a closed state. This closed state is achieved through subtle yet crucial movements in various loops within the enzyme, which are stabilized by interactions between active site residues, substrate and cofactor. In absence of interactions with the substrate and cofactor, the active site residues in the apo form of the enzyme are found to exhibit significant fluctuations. The current work reveals that three vital active site loops undergo conformational changes during the transition from the closed to open state. It may be noted that experimental studies comparing the crystal structures of apo and holo forms of SHMT have revealed domain movement upon substrate binding. Our study not only verifies the presence of this domain movement but also provides an in-depth analysis of the microenvironmental changes during the conformational transition.

We studied the conformational changes of serine hydroxymethyltransferase in apo and holo states. Three key active site loops, loop 1 (128–142), loop 2 (356–369), and loop 3 (48–68) play a crucial role in these transitions. In the holo form, Ser34 and Arg371 form hydrogen bonds with the PLP-SER complex, stabilizing these loops. In the apo form, the absence of these interactions induces chain movements, that affects distant structural regions. Specifically, Arg371 influences loop2 (356–369), while Ser34 affects loop3 (48–68). Hydrogen bonds and salt bridges are depicted as red and blue dashed lines.