2YPC: Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation H309S, crystallized with 2',3-(SP)-Cyclic-AMPS

2H phosphoesterases catalyze reactions on nucleotide substrates and contain two conserved histidine residues in the active site. Very limited information is currently available on the details of the active site and substrate/product binding during the catalytic cycle of these enzymes. We performed a comprehensive X-ray crystallographic study of mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase), a membrane-associated enzyme present at high levels in the tetrapod myelin sheath. We determined crystal structures of the CNPase phosphodiesterase domain complexed with substrate, product, and phosphorothioate analogues. The data provide detailed information on the CNPase reaction mechanism, including substrate binding mode and coordination of the nucleophilic water molecule. Linked to the reaction, an open/close motion of the beta5-alpha7 loop is observed. The role of the N terminus of helix alpha7--unique for CNPase in the 2H family--during the reaction indicates that 2H phosphoesterases differ in their respective reaction mechanisms despite the conserved catalytic residues. Furthermore, based on small-angle X-ray scattering, we present a model for the full-length enzyme, indicating that the two domains of CNPase form an elongated molecule. Finally, based on our structural data and a comprehensive bioinformatics study, we discuss the conservation of CNPase in various organisms.
PDB ID: 2YPCDownload
MMDB ID: 111573
PDB Deposition Date: 2012/10/30
Updated in MMDB: 2013/11
Experimental Method:
x-ray diffraction
Resolution: 1.894  Å
Source Organism:
Similar Structures:
Biological Unit for 2YPC: monomeric; determined by author and by software (PISA)
Molecular Components in 2YPC
Label Count Molecule
Protein (1 molecule)
2', 3'-cyclic Nucleotide 3'-phosphodiesterase(Gene symbol: Cnp)
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB