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3CJA

Structure of Rattus norvegicus NTPDase2 in complex with calcium and AMPPNP

Summary for 3CJA
Entry DOI10.2210/pdb3cja/pdb
Related3CJ1 3CJ7 3CJ9
DescriptorEctonucleoside triphosphate diphosphohydrolase 2, CALCIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... (4 entities in total)
Functional Keywordshydrolase, alpha/beta protein, actin-like fold, alternative splicing, calcium, glycoprotein, magnesium, membrane, transmembrane
Biological sourceRattus norvegicus (Norway rat)
Cellular locationMembrane; Multi-pass membrane protein (Potential): O35795
Total number of polymer chains1
Total formula weight51158.22
Authors
Zebisch, M.,Strater, N. (deposition date: 2008-03-12, release date: 2008-04-29, Last modification date: 2024-10-30)
Primary citationZebisch, M.,Strater, N.
Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling
Proc.Natl.Acad.Sci.Usa, 105:6882-6887, 2008
Cited by
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.
PubMed: 18458329
DOI: 10.1073/pnas.0802535105
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.1 Å)
Structure validation

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