Palmitoyl protein thioesterase: Difference between revisions

The <scene name='57/573128/3/1'>hydrophobic binding groove</scene> where palmitate binds is located in the second domain of PPT1. (<scene name='48/489312/Binding_groove/4'>This alternate view</scene> shows the protein-ligand complex in the same orientation as Figure 1 above for better comparison). The fact that palmitate has to <scene name='57/573128/6/1'>bend</scene> to fit into the binding pocket suggests that this pocket is designed to bind an unsaturated fatty acid, with a possible cis-double bond between C4 and C5 (Figure 1)<ref name="RSCB"/>. The top portion of the groove is formed by the residues from α2 to α3. The acid binds in a [https://en.wikipedia.org/wiki/Gauche_effect gauche conformation] creating a <scene name='58/580839/Kink_in_acid/1'>kink </scene> in the acid chain. This bending suggests that PPT-1 was originally designed to react with an unsaturated fatty acid with cis-double bonds. Several residues that are present near the active site create the rest of the groove, including <scene name='57/573128/10/1'>Ile235, Val236, Gln116, Gly40, and Met41</scene><ref name="RSCB"/>.