Figure 3

The minimum binding sequence in Myb1 and the complex structure of TvCyP1 with the same. (a) Binding curves from fluorescence polarization experiments of Myb1 fragments with TvCyP1. Error bars are standard deviation (SD). Binding affinities were derived from a one-site binding model by using GraphPad Prism 6. ¹⁰⁴EYGPKWNK¹¹¹ (Myb1^104–111) showed the highest binding affinity to TvCyP1 (16.81 ± 0.58 μM). (b) Electrostatic surface of TvCyP1 dimer in complex with the minimum binding sequence of Myb1, Myb1^104–111 (shown as green and magenta sticks; PDB: 5YBA). Each protomer binds to one molecule of Myb1 peptide. Although the peptide used was Myb1^104–111, electron densities of only ¹⁰⁵YGPKWN¹¹⁰ (protomer I) and ¹⁰⁴EYGPK¹⁰⁸ (protomer II) were obtained in the complex structure. Intramolecular salt bridge interaction between K108 and E104 is shown as a green dashed line (in ¹⁰⁴EYGPK¹⁰⁸ bound to protomer II). (c and d) Close-up views of interactions between TvCyP1 and Myb1 peptide. Residues of TvCyP1 interacting with Myb1 peptide are shown as orange sticks. Fragments of Myb1 peptide, ¹⁰⁵YGPKWN¹¹⁰ and ¹⁰⁴EYGPK¹⁰⁸, bound to either protomer, are represented as green and magenta sticks in (c) and (d), respectively. The hydrogen bond between the C=O of P107 and the side chain NH₂ of the catalytic residue R63 is shown as a black dashed line. See Supplementary Fig. S2 for a close-up view of the conformation of the Myb1 peptide bound to either protomer and the conformation of the same sequence in Myb1^35–141. See Supplementary Fig. S3 also for a 2D diagram by Ligplot+ showing detailed interactions between Myb1 peptide and TvCyP1.