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Figure 4 | BMC Structural Biology

Figure 4

From: Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly

Figure 4

Comparison of 'Leu intercalation' loops in vvUDG and E. coli UDG. This figure shows a structural comparison of the 'Leu intercalation' loops in vvUDG and E. coli UDG and provides a model for the lack of inhibition of vvUDG by Ugi. (A) Superimposition of 'Leu intercalation' loops. The two superimposed loops are shown in different colors (vvUDG cyan; E. coli UDG green). L191 in E. coli UDG (green) and the corresponding residue R185 in vvUDG (cyan) are shown as stick models. Other loop residues are also shown and some of the loop residues are labeled. It can be seen that only the two N-terminal loop residues, Pro (vvUDG P182; E. coli UDG P188) and His (vvUDG H181; E. coli UDG H187), are identical in sequence and in similar orientations. (B) Close-up view of UDG:Ugi complex. The structure of vvUDG was superimposed onto the E. coli UDG structure in the UDG:Ugi complex. For the UDG proteins only the loop regions are shown (E. coli UDG in green, vvUDG in cyan), while for Ugi the semi-transparent surface of the binding pocket is shown (colored by element). The eight hydrophobic residues of Ugi (M24, V29, V32, I33, V43, M56, L58 and V71) that form the hydrophobic cavity and provide major interactions with the 'Leu intercalation' loop in E. coli UDG [19] are shown as stick models. The corresponding residues in the 'Leu intercalation' loop, L191 in E. coli UDG (green) and R185 in vvUDG (cyan), are shown as stick models. In E. coli UDG:Ugi complex L191 points into the hydrophobic pocket.

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