Architecture of Y-Family DNA Polymerases Relevant to Translesion DNA Synthesis as Revealed in Structural and Molecular Modeling Studies
Figure 3
Structures of regions of ecDNAP IV (a), ecUmuC(V) (b), hDNAP (c), scDNAP (d). (a) View from the minor groove side of DNAP IV (yellow), showing the “chimney” opening (cleft or hole), which is defined by the upper lip (turquoise, aa33–36), left lip (blue, aa73–76) and lower lip (dark blue, aa244–247). The chimney opening in DNAP IV is large enough to accommodate the pyrene moiety of +BP (red). In DNAP IV, the dG moiety of +BP can base pair comfortably with dCTP in the canonical S1-dNTP shape. (Neither the dG moiety of +BP nor the dCTP are visible.) The template (gray) and primer (brown) are also shown. (b) Models of UmuC(V) with no adduct (B/left) or +BP paired with dCTP in the canonical “chair-like” S1-dNTP shape (b/center) or +BP paired with dCTP in the non-canonical, “goat-tail-like” S2-dNTP shape (b/right). The chimney opening is small (b/left) and the pyrene moiety of +BP does not fit into the chimney such that the S1-dNTP shape is possible (b/center). In contrast, the pyrene moiety of +BP fits under the chimney opening in the case of pairing with dCTP in the S2-dCTP shape (b/right), because it sits lower down in the active site compared to S1-dNTP. (c) Regions of hDNAP . Y-Family DNAPs in the IV/κ-class have a glycine “flue-handle,” such as G131 (turquoise, c/left) in hDNAP G131 adopts /-angles that lead to upward curvature of the protein backbone in the chimney upper lip (red arrow, c/left) and results in the “flue” amino acids (S132/M133, blue, c/center) pointing away from the chimney, giving a large opening. The c/right structure shows V130 (white) that serves as a scaffold to organize the chimney’s upper lip and left lip (yellow ribbons), along with the roof-aa (S137, purple), the steric gate (Y112, red) and a conserved tyrosine (Y174, brown), which stacks on the backbone of the left lip and helps orient it. V130 forms a square with the G131 flue-handle, L136 (gray) and the S137 roof (pink) upon which I166 stacks (dark gray). (d) Regions in scDNAP . Y-Family DNAPs in the V/η class have a bulky “flue-handle,” such as V54 in scDNAP η (turquoise, d/left), which causes downward curvature of the chimney upper lip (red arrow, d/center), and results in the “flue” amino acids (Q33/W34, blue, d/center) plugging the chimney, giving a small opening. The structure in d/right shows scaffold C53 (white) organizing the chimney’s upper lip and left lip (green ribbons in (c)), along with the roof-aa (I60, purple), the steric gate (F35, red) and a conserved tyrosine (Y131, brown), which stacks on the backbone of the left lip and orients it. C53 forms a square with the V54 flue-handle (turquoise), I59 (gray) and the I60 roof (pink). scDNAP has a large insert/loop (aa96–126) in the left lip, which is represented as a discontinuity. (e) The upper lip for hDNAP (yellow) is superimposed on the upper lip for scDNAP (green), which clearly shows the differences in curvature. X-ray coordinates are from 2OH2 for hDNAP [29] and from 1JIH for scDNAP [27], where hydrogens were added using insightII.
