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. 2022 Dec 5;19(6):1711–1732. doi: 10.1080/15548627.2022.2151294

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© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — PINK1^G411A improves relative positioning of ATP and substrate residue S65 within the active site. (A) Schematic representation of the entire human PINK1 protein including the mitochondrial targeting sequence (MTS), transmembrane region (TM) and N-terminal region (NT). Individual domains of the catalytically active fragment (aa 156–581) studied are color-coded: N- and C-lobes of the kinase domain in cyan and magenta, respectively; C-terminal domain (CTD) in blue. The three unique insertion loops are highlighted in yellow. Position 411 and the autophosphorylation site S228 are indicated. (B) 3D representation of the human PINK1 model with ATP shown in spheres. (C) 3D representation of the human PINK1 model with Ub bound shown as a green Connolly surface and ATP in stick representation. (D) The model is rotated 90° about the 45° -y/+x bisector, relative to (C). All components are represented as Connolly surfaces to indicate optimal packing was achieved. (E) Close-up of the PINK1, ATP, and Ub interface, with interacting residues represented as sticks. (F-G) Overlay of reduced representations of the different enzyme-substrate combinations with matching structures color-coded and aligned by (F) PINK1 variant or (G) substrate S65. PINK1 residues C388-Y431 containing the activation segment are depicted as ribbons and position 411, ATP, and S65 of the Ub substrates are shown in licorice stick rendering. (F) Positioning of S65 relative to WT PINK1, PINK1^G411A, PINK1^G411S, and PINK1^p-^S411 are shown from left to right and color-coded according to the substrates: Ub (yellow), p-S65-Ub (lime green), Ub-CR (magenta), and p-S65-Ub-CR (cyan). For PINK1^G411A, note the alignment for ATP and the oxygen atom of S65 of both Ub and Ub-CR. (G) Positioning of PINK1 and residues 411 relative to the respective S65 residues of Ub, p-S65-Ub, Ub-CR, and p-S65-Ub-CR are shown from left to right and color-coded according to the PINK1 variant: G411 (gray), A411 (salmon), S411 (purple), and p-S411 (olive). For Ub-CR, note the almost identical overlap for the activation segments of all PINK1 variants.