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Nature Chemical Biology 4, 557–563 (1 September 2008) | doi:10.1038/nchembio.104

|[beta]|-Lactone probes identify a papain-like peptide ligase in Arabidopsis thaliana

Zheming Wang , Christian Gu , Tom Colby , Takayuki Shindo , Rengarajan Balamurugan , Herbert Waldmann , Markus Kaiser & Renier A L van der Hoorn

New activity-based probes are essential for expanding studies on the hundreds of serine and cysteine proteases encoded by the genome of Arabidopsis thaliana. To monitor protease activities in plant extracts, we generated biotinylated peptides containing a β-lactone reactive group. These probes cause strong labeling in leaf proteomes. Unexpectedly, labeling was detected at the N terminus of PsbP, nonproteolytic protein of photosystem II. Inhibitor studies and reverse genetics led to the discovery that this unusual modification is mediated by a single plant-specific, papain-like protease called RD21. In cellular extracts, RD21 accepts both β-lactone probes and peptides as donor molecules and ligates them, probably through a thioester intermediate, to unmodified N termini of acceptor proteins.