2YPC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.894 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystallographic Analysis of the Reaction Cycle of 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase, a Unique Member of the 2H Phosphoesterase Family

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

(2013) J.Mol.Biol. 425: 4307

  • DOI: 10.1016/j.jmb.2013.06.012
  • Primary Citation of Related Structures:  

  • PubMed 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 th ...

    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.


    Organizational Affiliation

    Department of Biochemistry, University of Oulu, FIN-90014 Oulu, Finland; Biocenter Oulu, University of Oulu, FIN-90014 Oulu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2', 3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE
A
221Mus musculusMutation(s): 1 
Gene Names: Cnp (Cnp1)
EC: 3.1.4.37
Find proteins for P16330 (Mus musculus)
Go to UniProtKB:  P16330
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QQX
Query on QQX

Download SDF File 
Download CCD File 
A
[(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanyl-2-sulfanylidene-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol
ADENOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
C10 H12 N5 O5 P S
OMSUUENXGWGOLC-LHKKBNDGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.894 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.280α = 90.00
b = 47.490β = 94.89
c = 53.760γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references
  • Version 1.2: 2013-11-13
    Type: Database references
  • Version 1.3: 2015-07-15
    Type: Data collection
  • Version 1.4: 2018-03-07
    Type: Data collection, Source and taxonomy