5C7T | pdb_00005c7t

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

• PDB DOI: https://doi.org/10.2210/pdb5C7T/pdb

• Classification: HYDROLASE
• Organism(s): Bdellovibrio bacteriovorus HD100
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2015-06-24 Released: 2016-01-20 
• Deposition Author(s): Gabelli, S.B., de la Pena, A.H., Suarez, A., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.245 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

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

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.

(2015) PLoS One 10: e0141716-e0141716

• PubMed: 26524597 
• DOI: https://doi.org/10.1371/journal.pone.0141716
• Primary Citation Related Structures: 
  5C7Q, 5C7T, 5C8L


• 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.

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Organizational 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.
Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
Biology Department, Loyola University Maryland, Baltimore, Maryland, United States of America.
Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
Department of Medical and Research Technology, University of Maryland 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; 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.3 kDa 
• Atom Count: 3,365 
• Modeled Residue Count: 361 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NudF protein	A, B	182	Bdellovibrio bacteriovorus HD100	Mutation(s): 1  Gene Names: nudF, Bd3179 EC: 3.6.1.13
UniProt
Find proteins for Q6MIH8 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MIH8  Go to UniProtKB:  Q6MIH8

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR	C [auth A], O [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N
PGE	T [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0	J [auth A]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
PEG	N [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], K [auth A], L [auth A], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.245 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.594	α = 90
b = 103.402	β = 90
c = 51.623	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Gabelli, S.B., de la Pena, A.H., Suarez, A., Amzel, L.M.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description