Figure 3: IAA6 and IAA19 exhibit high intrinsic disorder offering a broad ubiquitylation zone with likely limited lysine availability.

(a) Putative lysine ubiquitylation in IAA6 and IAA19 concentrate in hotspots with low compactness. Meta-structure of IAA6 and IAA19 was quantified by sequence-derived parameters, compactness and local secondary structure. Residue-specific compactness is displayed in green-orange (IAA6), and blue-orange (IAA19) 2-colour sequential variation (see colour key), where folding corresponds to values above 300 from DisProt database (see Supplementary Fig. 14 for details). IAA6 and IAA19 IVU samples were analysed via LC-MS and putative ubiquitylation sites were mapped relative to their domain structure (black boxes). (b) List of Ub-modified IAA6 (green) and IAA19 (blue) peptides and their ion scores (Mascot¹) identified by mass spectrometry. Specific ubiquitylated Lys-residues of cleaved peptides are shown in red, and (§) symbol depicts the site is also covered by the Lys-Arg-Gly-Gly (LRGG) remnant, which is further confirmation that the site is genuine. Ub-conjugation on Lys111 in IAA19 (ref. 2) is also supported by the LRGG remnant, reducing the uncertainty caused by the N-terminal location on the peptide. See Supplementary Figs. 11 and 12 for information about reproducibility and FDR. (c) Distribution of identified ubiquitin linkage types. IVU reactions for IAA6 (green) and IAA19 (blue) with or without IAA were analysed via LC-MS, and ubiquitin peptides corresponding to different ubiquitin linkage types were identified (for details see Supplementary Fig. 13).