1GA7

CRYSTAL STRUCTURE OF THE ADP-RIBOSE PYROPHOSPHATASE IN COMPLEX WITH GD+3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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.


    Related Citations: 
    • The Versatility of the Nudix Hydrolases as Revealed by the ADP-ribose Pyrophosphatase
      Gabelli, S.B., Bianchet, M.A., Bessman, M.J., Amzel, L.M.
      (2000) Thesis --: 1

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL 23.7 KDA PROTEIN IN ICC-TOLC INTERGENIC REGIONA, B209Escherichia coliMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93K97
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD3
Query on GD3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
GADOLINIUM ION
Gd
RJOJUSXNYCILHH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.93α = 90
b = 67.89β = 90
c = 98.07γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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