Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks
Figure 4
Functional significance of loop based conserved high–energy interactions.
The figure depicts the presence of conserved interactions involving loops around the catalytic site in TIM fold. (a) TIM domain from 2mnr was taken as the representative structure for DGDL (c.1.11.2, see Table S1) family. Ligands obtained from close homologues (Protein Data Bank IDs: 1DTN, 1FHV, 1JCT, 1KKR, and 1MDL) were mapped onto 2mnr (after structural alignment of the individual TIM domain and 2mnr) and depicted as vdW spheres colored according to the atom types. The conserved high–energy interactions (f–PEN–20(0.8)) are represented as red spheres while the conserved low–energy interactions (f–ljPEN–8(0.8)) are represented in blue. The important E317 residue which acts as a general acid catalyst in concerted acid–base catalyzed formation of a stabilized enolic tautomer of mandelic acid [56] is highlighted in green. An alternate view of the barrel is given in (b). (c) shows the ternary complex of XIP–GH10–GH11 where the conserved high–energy loop interactions (f–PEN–20(0.8); the involved residues are highlighted as spheres) in XIP1 (gray cartoon) involved in the inhibitory interactions of GH10 and GH11 (cartoons; cyan and green respectively) at the Enzyme Binding Sites (EBS) are presented.