Fig. 5: Associations of differential ac-K turnover with structural and enzymatic events.

a–b Probability logos of acetylated lysine (ac-K) sites linked to slower turnover and ac-K sites responsive to lysine deacetylase inhibitors (KDACi) reported by Schölz et al. (red horizontal line: Bonferroni-corrected p-value of 0.05 indicating significant over- or underrepresentation). For the KDACi motif, only sites that showed at least a TWOfold regulation upon KDAC inhibition were included. Logos were generated using pLogo²⁹ (https://plogo.uconn.edu/). The background was defined by all sites quantified in the respective studies. c Potential model explaining the measured decrease in turnover on ac-K sites followed by a proline (KAT: lysine acetyltransferase; KDAC: lysine deacetylase). d Tukey-boxplots of log2 \({{{{{\rm{N}}}}}}/{{{{{\rm{P}}}}}}\) ratios or log10 \({{{{{\rm{K}}}}}}\) values for ENO1 and selected lysine sites (box borders: 1^st and 3^rd quartile; lines in boxes: medians; whiskers: ranging to greatest value within 1.5× interquartile range; dots: replicates; dashed line: median of protein \({{{{{\rm{N}}}}}}/{{{{{\rm{P}}}}}}\); *: significantly different turnover to protein or unmodified counterpart). Boxplots are based on n = 4 cell culture replicates, except for ac-K343 (n = 2). e–g Positioning of ac-K139, ac-K262, and ac-K343 in the ENO1 homodimer (PDB 3B97³³; black: carbon; red: oxygen; blue: nitrogen; gray: hydrogen; purple: Mg2+ ions). The PyMol plugin PyTMs was used to add acetyl moieties to lysine residues. h Tukey-boxplots of log2 \({{{{{\rm{N}}}}}}/{{{{{\rm{P}}}}}}\) ratios (description same as in panel d) and turnover curves (solid lines: means; shaded areas: 95 % confidence intervals) for EWSR1 and selected lysine sites. Plots are based on n = 4 cell culture replicates, except for ac-K641 (n = 3) and the box and label loss curve of ac-K439 (n = 1 and n = 2, respectively). K439 and K641 are located in the RNA-recognitions motif and the nuclear localization signal, respectively. For panels d and h, the number of peptides and spectra included in each plot varies for each site/protein and replicate and can be retrieved from Supplementary Data 1. Positions of post-translational modifications are given for the major protein isoform. Source data are provided as a Source Data file.