6G4G

Full length ectodomain of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) including the SMB domains but with a partially disordered active site structure

Summary for 6G4G

• Entry DOI: 10.2210/pdb6g4g/pdb
• Related: 6f2t
• Descriptor: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: enzyme, ectonucleotide phosphodiesterase/pyrophosphatase, complex, zinc, smb, pde, hydrolase
• Biological source: Rattus norvegicus (Rat)
• Total number of polymer chains: 4
• Total formula weight: 387204.00

Authors

Dohler, C.,Zebisch, M.,Strater, N. (deposition date: 2018-03-27, release date: 2018-11-07, Last modification date: 2024-10-23)

Primary citation

Dohler, C.,Zebisch, M.,Krinke, D.,Robitzki, A.,Strater, N.
Crystallization of ectonucleotide phosphodiesterase/pyrophosphatase-3 and orientation of the SMB domains in the full-length ectodomain.
Acta Crystallogr F Struct Biol Commun, 74:696-703, 2018

PubMed Abstract: Ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3, ENPP3) is an ATP-hydrolyzing glycoprotein that is located in the extracellular space. The full-length ectodomain of rat NPP3 was expressed in HEK293S GntI cells, purified using two chromatographic steps and crystallized. Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible. The SMB-like domains have the same orientation in all four molecules in the asymmetric unit. The SMB2 domain is oriented as in NPP2, but the SMB1 domain does not interact with the PDE domain but extends further away from the PDE domain. Deletion of the SMB domains resulted in crystals that diffracted to 2.4 Å resolution and are suitable for substrate-binding studies.

PubMed: 30387774
DOI: 10.1107/S2053230X18011111

Experimental method

X-RAY DIFFRACTION (2.8 Å)