5C7T: Crystal Structure Of The Bdellovibrio Bacteriovorus Nucleoside Diphosphate Sugar Hydrolase In Complex With Adp-ribose

Citation:
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 A Calpha 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 alpha-beta-alpha NDPSase fold differentiates NDPSases from ADPRases.
PDB ID: 5C7TDownload
MMDB ID: 135716
PDB Deposition Date: 2015/6/24
Updated in MMDB: 2016/01
Experimental Method:
x-ray diffraction
Resolution: 2.06  Å
Source Organism:
Similar Structures:
Biological Unit for 5C7T: dimeric; determined by author and by software (PISA)
Molecular Components in 5C7T
Label Count Molecule
Proteins (2 molecules)
2
Nudf Protein
Molecule annotation
Chemicals (18 molecules)
1
2
2
6
3
7
4
1
5
1
6
1
* Click molecule labels to explore molecular sequence information.

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