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Characterization of plant dipeptidyl-peptidases III from Physcomitrella patens and Arabidopsis thaliana

Plant dipeptidyl-peptidases III (DPPs III) have been recognized only recently, as data from plant genome sequencing projects have become available. The amino acid sequence showed them to be atypical compared to previously characterized DPPs III, as the signature active site motif of the DPP III family, the hexapeptide HEXXXH, is replaced by a pentapeptide HEXXH motif, common among many other zinc-metallopeptidases1. We have cloned, heterologuosly expressed, and purified DPPs III from Physcomitrella patens and Arabidopsis thaliana. Biochemical characterization by dipeptidyl-2-naphtylamide substrates has revealed significant differences between the two enzymes. Furthermore, we have changed the pentapeptide HECCH motif in Physcomitrella DPP III to HECCGH and HECLGH by site-directed mutagenesis and have shown that relatively low peptidase activity of this enzyme is not due to the hexapeptide motif replacement. The presence of a NUDIX domain on the N-terminus is an additional atypical characteristic, specific to plant DPPs III. This domain is found in proteins belonging to the Nudix hydrolase superfamily, which predominantly catalyze the hydrolysis of small nucleotide substrates composed of a nucleoside diphosphate linked to another moiety X. By bioinformatic analysis, due to its NUDIX domain, Arabidopsis DPP III was predicted to be an isopentenyl diphosphate isomerase (IDI)2. We have performed a functional color complementation assay of IDI activity and shown this prediction to be false. In addition, we discuss putative Nudix hydrolase activity of plant DPPs III based on similarity to characterized plant Nudix hydrolases. Since the biological function of plant DPPs III is currently unknown, our results represent a starting point for understanding of these novel and peculiar proteins. 1. Barrett, A. and Chen, J.-M. (2013) Dipeptidyl-peptidase III. In: Handbook of Proteolytic Enzymes, 3rd Edn. Rawlings, N.D. and Salvesen, G., (Eds) Amsterdam, The Netherlands, Elsevier Academic Press, pp.1285- 1289 2. Gunawardana, D., Likic, V.A., and Gayler, K.R. (2009) A comprehensive bioinformatics analysis of the Nudix superfamily in Arabidopsis thaliana. Compar. Funct. Genom. Article ID 820381

Arabidopsis thaliana ; enzyme kinetics ; metalloprotease ; Physcomitrella patens ; plant biochemistry ; substrate specificity

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