5C7T

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase in complex with ADP-ribose

Summary for 5C7T

• Entry DOI: 10.2210/pdb5c7t/pdb
• Related: 5C7Q
• Descriptor: NudF protein, ADENOSINE-5-DIPHOSPHORIBOSE, SULFATE ION, ... (8 entities in total)
• Functional Keywords: nudix, hydrolase
• Biological source: Bdellovibrio bacteriovorus
• Total number of polymer chains: 2
• Total formula weight: 45297.05

Authors

Gabelli, S.B.,de la Pena, A.H.,Suarez, A.,Amzel, L.M. (deposition date: 2015-06-24, release date: 2016-01-20, Last modification date: 2023-09-27)

Primary citation

de la Pena, A.H.,Suarez, A.,Duong-Ly, K.C.,Schoeffield, A.J.,Pizarro-Dupuy, M.A.,Zarr, M.,Pineiro, S.A.,Amzel, L.M.,Gabelli, S.B.
Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.
Plos One, 10:e0141716-e0141716, 2015

PubMed 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.

PubMed: 26524597
DOI: 10.1371/journal.pone.0141716

Experimental method

X-RAY DIFFRACTION (2.06 Å)