PDBsum entry 2ypc

Hydrolase

PDB id: 2ypc

Contents

Protein chain

214 a.a.

Ligands

QQX

Waters ×204

PDB id:

2ypc

Name:

Hydrolase

Title:

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation h309s, crystallized with 2',3-(sp)- cyclic-amps

Structure:

2', 3'-cyclic nucleotide 3'-phosphodiesterase. Chain: a. Fragment: c-terminal catalytic domain, residues 159-378. Synonym: cnp, cnpase. Engineered: yes. Mutation: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: rosetta.

Resolution:

1.89Å R-factor: 0.167 R-free: 0.213

Authors:

M.Myllykoski,A.Raasakka,M.Lehtimaki,H.Han,P.Kursula

Key ref:

M.Myllykoski et al. (2013). Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family. J Mol Biol, 425, 4307-4322. PubMed id: 23831225 DOI: 10.1016/j.jmb.2013.06.012

Date:

30-Oct-12 Release date: 10-Jul-13

Protein chain

P16330  (CN37_MOUSE) -  2',3'-cyclic-nucleotide 3'-phosphodiesterase from Mus musculus

Seq: 420 a.a.

Struc: 214 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.4.37 - 2',3'-cyclic-nucleotide 3'-phosphodiesterase.
• Reaction: a nucleoside 2',3'-cyclic phosphate + H2O = a nucleoside 2'-phosphate + H⁺

nucleoside 2',3'-cyclic phosphate (Bound ligand (Het Group name = QQX) matches with 45.83% similarity) + H2O = nucleoside 2'-phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.jmb.2013.06.012

J Mol Biol 425:4307-4322 (2013)

PubMed id: 23831225

Crystallographic analysis of the reaction cycle of 2',3'-cyclic nucleotide 3'-phosphodiesterase, a unique member of the 2H phosphoesterase family.

M.Myllykoski, A.Raasakka, M.Lehtimäki, H.Han, I.Kursula, P.Kursula.

ABSTRACT

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 β5-α7 loop is observed. The role of the N terminus of helix α7-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.