Structural and enzymatic characterization of a nucleoside diphosphate sugar hydrolase from Bdellovibrio bacteriovorus

Andres H. De La Peña, Allison Suarez, Krisna C. Duong-Ly, Andrew J. Schoeffield, Mario A. Pizarro-Dupuy, Melissa Zarr, Silvia A. Pineiro, L. Mario Amzel, Sandra B. Gabelli

Research output: Contribution to journalArticlepeer-review

Abstract

Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 - a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.

Original languageEnglish (US)
Article numbere141716
JournalPloS one
Volume10
Issue number11
DOIs
StatePublished - Nov 2 2015

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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