3CJ1 image
Deposition Date 2008-03-12
Release Date 2008-04-29
Last Version Date 2024-11-06
Entry Detail
PDB ID:
3CJ1
Keywords:
Title:
Structure of Rattus norvegicus NTPDase2
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Ectonucleoside triphosphate diphosphohydrolase 2
Gene (Uniprot):Entpd2
Chain IDs:A
Chain Length:456
Number of Molecules:1
Biological Source:Rattus norvegicus
Primary Citation
Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling
Proc.Natl.Acad.Sci.Usa 105 6882 6887 (2008)
PMID: 18458329 DOI: 10.1073/pnas.0802535105

Abstact

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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