Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 50.61 kDa 
• Atom Count: 3682 
• Modelled Residue Count: 419 
• Deposited Residue Count: 456 
• Unique protein chains: 1

3CJ1

Structure of Rattus norvegicus NTPDase2

• PDB DOI: 10.2210/pdb3CJ1/pdb

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


• Deposited: 2008-03-12 Released: 2008-04-29 
• Deposition Author(s): Zebisch, M., Strater, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling

Zebisch, M., Strater, N.

(2008) Proc Natl Acad Sci U S A 105: 6882-6887

• PubMed: 18458329 
• DOI: 10.1073/pnas.0802535105
• Primary Citation of Related Structures:  
  3CJ1, 3CJ7, 3CJ9, 3CJA


• PubMed Abstract: 
  

Cell surface-located nucleoside triphosphate diphosphohydrolases (NTPDase1, -2, -3, and -8) are oligomeric integral membrane proteins responsible for signal conversion and inactivation in extracellular nucleotide-mediated "purinergic" signaling. They catalyze the sequential hydrolysis of the signaling molecule ATP via ADP to AMP. Here we present the structure of the extracellular domain of Rattus norvegicus NTPDase2 in an active state at resolutions between 1.7 A and 2.1 A in four different forms: (i) apo form, (ii) ternary complex with the nonhydrolyzable ATP analog AMPPNP and cofactor Ca(2+), (iii) quaternary complex with Ca(2+) and bound products AMP and phosphate, and (iv) binary product complex with AMP only. Analysis of the ATP (analog) binding mode explains the importance of several residues for activity and allows suggestion of a catalytic mechanism. The carboxylate group of E165 serves as a catalytic base and activates a water molecule, which is well positioned for nucleophilic attack on the terminal phosphate. Based on analysis of the two product complex structures in which AMP adopts different conformations, a substrate binding mode for ADP hydrolysis is proposed. This allows for an understanding of how the same hydrolytic site can be engaged in ATP and ADP but not AMP hydrolysis.

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Organizational Affiliation: 

Center for Biotechnology and Biomedicine, Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ectonucleoside triphosphate diphosphohydrolase 2	A	456	Rattus norvegicus	Mutation(s): 0  Gene Names: Entpd2, Cd39l1 EC: 3.6.1.5 (PDB Primary Data), 3.6.1 (UniProt)
UniProt
Find proteins for O35795 (Rattus norvegicus) Explore O35795  Go to UniProtKB:  O35795

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.346	α = 90
b = 69.029	β = 90
c = 164.248	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-12 
• Released Date: 2008-04-29 
Deposition Author(s): Zebisch, M., Strater, N.

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance