title: Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.
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.
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America; Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Andres H
authors.initials: AH
authors.lastname: de la Peña
authors.affiliation: Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Allison
authors.initials: A
authors.lastname: Suarez
authors.affiliation: Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Krisna C
authors.initials: KC
authors.lastname: Duong-Ly
authors.affiliation: Biology Department, Loyola University Maryland, Baltimore, Maryland, United States of America.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Schoeffield
authors.affiliation: Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Mario A
authors.initials: MA
authors.lastname: Pizarro-Dupuy
authors.affiliation: Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Melissa
authors.initials: M
authors.lastname: Zarr
authors.affiliation: Department of Medical and Research Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Silvia A
authors.initials: SA
authors.lastname: Pineiro
authors.affiliation: Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: L Mario
authors.initials: LM
authors.lastname: Amzel
authors.affiliation: Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
authors.forename: Sandra B
authors.initials: SB
authors.lastname: Gabelli
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001501:Bdellovibrio / Q000201:enzymology* / Q000235:genetics; D020134:Catalytic Domain; D003001:Cloning, Molecular; D008958:Models, Molecular; D009702:Nucleoside Diphosphate Sugars / Q000378:metabolism; D019897:Periplasm / Q000378:metabolism; D017434:Protein Structure, Tertiary; D011755:Pyrophosphatases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D000096964:Nudix Hydrolases
chemical_list: D001426:Bacterial Proteins; D009702:Nucleoside Diphosphate Sugars; D011755:Pyrophosphatases; D000096964:Nudix Hydrolases