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Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies

Fig 2

Structural analysis of loop 7 in A3G-ssDNA interaction.

A) Overview of the A3GCTD, shown in gray surface representation, bound to an adenine in the -1 nucleotide-binding pocket, shown in light blue sticks. Selected A3GCTD residues in the pocket are shown in teal sticks. B) The backbones of I314 and P210 form hydrogen bonds with the adenosine (shown in light blue) in the -1 nucleotide pocket. W211, W285, and Y315 stack with the nucleotide to stabilize it in the pocket. C) Structural alignment of the A3GCTD (teal) to A3A (magenta, PDBID 5SWW) [31], shows that conserved residues W285, I314, and Y315 of the -1 nucleotide-binding pocket are held in similar positions. D) Comparison of the A3GCTD, teal, to the A3A-DNA complex, magenta (PDBID 5SWW) [31]. In the A3A structure, D131 forms a hydrogen bond with the Watson-Crick edge of the hotspot nucleotide thymidine (light pink). In the A3GCTD structure, D316 and D317 are flipped 180 degrees to avoid clashing with the non-preferred adenine (light blue). The flipped conformation is similar to that of the apo structure of the A3GCTD, green (PDBID 3IR2) [24].

Fig 2