Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor

Masaru Gotoa Department of Molecular Bioscience, Toho University, Japan

https://orcid.org/0000-0002-9317-0521 View further author information

Natsumi Sakamotob Department of Chemistry, Toho University, JapanView further author information

Shoko Higashib Department of Chemistry, Toho University, JapanView further author information

Rena Kawataa Department of Molecular Bioscience, Toho University, JapanView further author information

Kazuki Nagatsua Department of Molecular Bioscience, Toho University, JapanView further author information

Ryota Saitob Department of Chemistry, Toho University, Japan;c Research Center for Materials with Integrated Properties, Toho University, JapanCorrespondence[email protected]
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Figures & data

Figure 1. Structures of the pterin-based RTA inhibitors with peptide pendants.

Table 1. Data collection, processing, and refinement statisticsTable Footnote^†.

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Figure 2. Synthesis of N-(pterin-7-carbonyl)glycyl-L-tyrosine (7PCGY).

Figure 3. X-ray crystal structures of ricin toxin A chain (RTA) with or without the pterin-based inhibitors. (A) Omit map for bound N-(pterin-7-carbonyl)glycyl-L-tyrosine (7PCGY). F_o–F_c electron density (shown with black baskets) contoured to 2σ showing evidence for 7PCGY bound to this region. The omit map was generated by removing the ligand from the structure. This image was created using PyMOLCitation²⁷. (B) Surface representation of the 7PCGY/RTA complex. The RTA surface is shown as an atomic charge map. (C) The interactions of 7PCGY in the catalytic primary pocket of RTA observed in the crystal structure of the 7PCGY/RTA complex. Conventional hydrogen bonds are represented as cyan dashed lines, hydrogen bonds between CH and carbonyl oxygen are represented as yellow dashed lines and aromatic (π-π and T-shaped) interactions are represented as magenta dashed lines. (D) Superimposition of protein crystal structures of 7PCGY/RTA (grey) and a ligand-free RTA (PDBID: 1RTC, orange). (E) X-ray crystal structure of the 7PCGF/RTA complex (PDBID: 4HUO). Conventional hydrogen bonds are represented as cyan dashed lines, hydrogen bonds between CH and carbonyl oxygen are represented as yellow dashed lines and aromatic (π-π and T-shaped) interactions are represented as magenta dashed lines. (F) A comparison of crystal structures of 7PCGY/RTA and 7PCGF/RTA. The protein portion of 7PCGY/RTA is shown in grey and that of 7PCGF/RTA in medium blue. All image creations, except (A), and interaction detections were performed using the Discovery Studio VisualiserCitation²⁸.

Table 2. Interactions between pterin-based inhibitors and RTA.

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Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor

Table 1. Data collection, processing, and refinement statisticsTable Footnote^†.

Table 2. Interactions between pterin-based inhibitors and RTA.

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Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor

Figures & data

Table 1. Data collection, processing, and refinement statisticsTable Footnote†.

Table 2. Interactions between pterin-based inhibitors and RTA.

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Table 1. Data collection, processing, and refinement statisticsTable Footnote^†.