Fig. 7: Schematic representation of the XPD translocation mechanism on ssDNA. | Nature Communications

Fig. 7: Schematic representation of the XPD translocation mechanism on ssDNA.

From: Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology

Fig. 7: Schematic representation of the XPD translocation mechanism on ssDNA.

The four domains of XPD are color-coded as follows: RecA1 (gold), RecA2 (blue), Arch (magenta), and Fe–S (green). The ssDNA is depicted in cyan. Key structural elements of XPD controlling DNA translocation are shown in the middle of the figure, including Constriction 1, Constriction 2 (black dashed circles) and the ATPase cleft (black dashed rectangle). Marker 1 in red and Marker 2 in navy blue are clearly labeled at the entry point to Constriction 1 and Constriction 2, respectively. Changes in nucleotide state are labeled above the arrows denoting the respective conformational transitions. For each translocation step, the XPD constriction engaged in tightly ssDNA binding is indicated by a light green dashed circle. The directions of the large-scale domain motions are indicated by arrows, each matching the color of the corresponding moving domain.

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