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Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.

de la Peña AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Recognition of ADPR by Bd-NDPSase.A) Ribbon representation of the catalytic site of the ADPR-bound E140Q Bd-NDPSase crystal structure (PDB ID 5C7T). B) Schematic representation of the recognition of ADPR by Bd-NDPSase. Catalytic helix (α1) residues are shown in cyan, catalytic loop L9 residues are shown in magenta. N-terminal domain residues (1–44) are shown in green as is the specificity loop L7. Hydrogen bonds are shown as orange dashes. The prime symbol (‘) denotes residues of the opposite monomer.
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pone.0141716.g004: Recognition of ADPR by Bd-NDPSase.A) Ribbon representation of the catalytic site of the ADPR-bound E140Q Bd-NDPSase crystal structure (PDB ID 5C7T). B) Schematic representation of the recognition of ADPR by Bd-NDPSase. Catalytic helix (α1) residues are shown in cyan, catalytic loop L9 residues are shown in magenta. N-terminal domain residues (1–44) are shown in green as is the specificity loop L7. Hydrogen bonds are shown as orange dashes. The prime symbol (‘) denotes residues of the opposite monomer.

Mentions: Adenosine recognition involves hydrogen bonding by the E38’ (prime denotes a residue of the other monomer) main chain amide nitrogen and carbonyl oxygen to the adenosyl N1 and N6 respectively. The main chain oxygen of G115’ bridges the adenosyl N6 and N7. R37’ and Y19 flank the nucleoside base though stacking interactions on opposite sides (Figs 4 and 5A). Analogous stacking interactions, involving the absolutely conserved arginine on strand β3 and the conserved aromatic residue on loop L1 are also present in Ec-NDPSase and Ec-ADPRase (Fig 5).


Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus.

de la Peña AH, Suarez A, Duong-Ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB - PLoS ONE (2015)

Recognition of ADPR by Bd-NDPSase.A) Ribbon representation of the catalytic site of the ADPR-bound E140Q Bd-NDPSase crystal structure (PDB ID 5C7T). B) Schematic representation of the recognition of ADPR by Bd-NDPSase. Catalytic helix (α1) residues are shown in cyan, catalytic loop L9 residues are shown in magenta. N-terminal domain residues (1–44) are shown in green as is the specificity loop L7. Hydrogen bonds are shown as orange dashes. The prime symbol (‘) denotes residues of the opposite monomer.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4629899&req=5

pone.0141716.g004: Recognition of ADPR by Bd-NDPSase.A) Ribbon representation of the catalytic site of the ADPR-bound E140Q Bd-NDPSase crystal structure (PDB ID 5C7T). B) Schematic representation of the recognition of ADPR by Bd-NDPSase. Catalytic helix (α1) residues are shown in cyan, catalytic loop L9 residues are shown in magenta. N-terminal domain residues (1–44) are shown in green as is the specificity loop L7. Hydrogen bonds are shown as orange dashes. The prime symbol (‘) denotes residues of the opposite monomer.
Mentions: Adenosine recognition involves hydrogen bonding by the E38’ (prime denotes a residue of the other monomer) main chain amide nitrogen and carbonyl oxygen to the adenosyl N1 and N6 respectively. The main chain oxygen of G115’ bridges the adenosyl N6 and N7. R37’ and Y19 flank the nucleoside base though stacking interactions on opposite sides (Figs 4 and 5A). Analogous stacking interactions, involving the absolutely conserved arginine on strand β3 and the conserved aromatic residue on loop L1 are also present in Ec-NDPSase and Ec-ADPRase (Fig 5).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.