Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 48.51 kDa 
• Atom Count: 3562 
• Modelled Residue Count: 407 
• Deposited Residue Count: 418 
• Unique protein chains: 1

1G9Q

COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE

• PDB DOI: 10.2210/pdb1G9Q/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-11-27 Released: 2001-05-02 
• Deposition Author(s): Gabelli, S.B., Bianchet, M.A., Bessman, M.J., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family.

Gabelli, S.B., Bianchet, M.A., Bessman, M.J., Amzel, L.M.

(2001) Nat Struct Biol 8: 467-472

• PubMed: 11323725 
• DOI: 10.1038/87647
• Primary Citation of Related Structures:  
  1G0S, 1G9Q, 1GA7


• PubMed Abstract: 
  

Regulation of cellular levels of ADP-ribose is important in preventing nonenzymatic ADP-ribosylation of proteins. The Escherichia coli ADP-ribose pyrophosphatase, a Nudix enzyme, catalyzes the hydrolysis of ADP-ribose to ribose-5-P and AMP, compounds that can be recycled as part of nucleotide metabolism. The structures of the apo enzyme, the active enzyme and the complex with ADP-ribose were determined to 1.9 A, 2.7 A and 2.3 A, respectively. The structures reveal a symmetric homodimer with two equivalent catalytic sites, each formed by residues of both monomers, requiring dimerization through domain swapping for substrate recognition and catalytic activity. The structures also suggest a role for the residues conserved in each Nudix subfamily. The Nudix motif residues, folded as a loop-helix-loop tailored for pyrophosphate hydrolysis, compose the catalytic center; residues conferring substrate specificity occur in regions of the sequence removed from the Nudix motif. This segregation of catalytic and recognition roles provides versatility to the Nudix family.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGION	A, B	209	Escherichia coli	Mutation(s): 0  Gene Names: ORF209 EC: 3.6.1.13
UniProt
Find proteins for Q93K97 (Escherichia coli (strain K12)) Explore Q93K97  Go to UniProtKB:  Q93K97

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APR	C [auth B], D [auth B]	ADENOSINE-5-DIPHOSPHORIBOSE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-KEOHHSTQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.93	α = 90
b = 67.89	β = 90
c = 98.07	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-11-27 
• Released Date: 2001-05-02 
Deposition Author(s): Gabelli, S.B., Bianchet, M.A., Bessman, M.J., Amzel, L.M.

Revision History  

• Version 1.0: 2001-05-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-08
  Changes: Structure summary