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Licensed Unlicensed Requires Authentication Published by De Gruyter July 28, 2016

A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III

  • Zrinka Karačić , Bojana Vukelić , Gabrielle H. Ho , Iva Jozić , Iva Sučec , Branka Salopek-Sondi , Marija Kozlović , Steven E. Brenner , Jutta Ludwig-Müller and Marija Abramić EMAIL logo
From the journal Biological Chemistry

Abstract

In a search for plant homologues of dipeptidyl peptidase III (DPP III) family, we found a predicted protein from the moss Physcomitrella patens (UniProt entry: A9TLP4), which shared 61% sequence identity with the Arabidopsis thaliana uncharacterized protein, designated Nudix hydrolase 3. Both proteins contained all conserved regions of the DPP III family, but instead of the characteristic hexapeptide HEXXGH zinc-binding motif, they possessed a pentapeptide HEXXH, and at the N-terminus, a Nudix box, a hallmark of Nudix hydrolases, known to act upon a variety of nucleoside diphosphate derivatives. To investigate their biochemical properties, we expressed heterologously and purified Physcomitrella (PpND) and Arabidopsis (AtND) protein. Both hydrolyzed, with comparable catalytic efficiency, the isopentenyl diphosphate (IPP), a universal precursor for the biosynthesis of isoprenoid compounds. In addition, PpND dephosphorylated four purine nucleotides (ADP, dGDP, dGTP, and 8-oxo-dATP) with strong preference for oxidized dATP. Furthermore, PpND and AtND showed DPP III activity against dipeptidyl-2-arylamide substrates, which they cleaved with different specificity. This is the first report of a dual activity enzyme, highly conserved in land plants, which catalyzes the hydrolysis of a peptide bond and of a phosphate bond, acting both as a dipeptidyl peptidase III and an atypical Nudix hydrolase.

Acknowledgments

Support for this study by the Alexander von Humboldt foundation (project name: ‘Study of plant enzymes from metallopeptidase families M20 and M49’), by the Croatian Science Foundation (project number 7235: ‘Flexibility, activity and structure correlations in the dipeptidyl peptidase III family’) and NIH R01 GM071749 (to S.E.B.) is gratefully acknowledged. We thank Francis X. Cunningham, Jr., for his generous gift of pAC-BETA and pTrcAtipi plasmids, and Annsea Park for valued guidance.

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Supplemental Material:

The online version of this article (DOI: 10.1515/hsz-2016-0141) offers supplementary material, available to authorized users.


Received: 2016-2-20
Accepted: 2016-7-25
Published Online: 2016-7-28
Published in Print: 2017-1-1

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