4WFR

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation T232A, complexed with 2'-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase.

Raasakka, A.Myllykoski, M.Laulumaa, S.Lehtimaki, M.Hartlein, M.Moulin, M.Kursula, I.Kursula, P.

(2015) Sci Rep 5: 16520-16520

  • DOI: 10.1038/srep16520
  • Primary Citation of Related Structures:  
    4WEX, 4WFR, 4WC9, 4WBI, 4WBL, 4WCA, 4WCB, 4WCC, 4WDA, 4WDB

  • PubMed Abstract: 
  • 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydroly ...

    2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydrolysis of nucleoside 2',3'-cyclic monophosphates to nucleoside 2'-monophosphates. The detailed reaction mechanism and the essential catalytic amino acids involved have been described earlier, but the roles of many amino acids in the vicinity of the active site have remained unknown. Here, several CNPase catalytic domain mutants were studied using enzyme kinetics assays, thermal stability experiments, and X-ray crystallography. Additionally, the crystal structure of a perdeuterated CNPase catalytic domain was refined at atomic resolution to obtain a detailed view of the active site and the catalytic mechanism. The results specify determinants of ligand binding and novel essential residues required for CNPase catalysis. For example, the aromatic side chains of Phe235 and Tyr168 are crucial for substrate binding, and Arg307 may affect active site electrostatics and regulate loop dynamics. The β5-α7 loop, unique for CNPase in the 2H phosphoesterase family, appears to have various functions in the CNPase reaction mechanism, from coordinating the nucleophilic water molecule to providing a binding pocket for the product and being involved in product release.


    Organizational Affiliation

    Helmholtz Centre for Infection Research at German Electron Synchrotron (DESY), Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2',3'-cyclic-nucleotide 3'-phosphodiesteraseA221Mus musculusMutation(s): 1 
Gene Names: CnpCnp1
EC: 3.1.4.37
Find proteins for P16330 (Mus musculus)
Explore P16330 
Go to UniProtKB:  P16330
NIH Common Fund Data Resources
IMPC  MGI:88437
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2AM
Query on 2AM

Download CCD File 
A
ADENOSINE-2'-MONOPHOSPHATE
C10 H14 N5 O7 P
QDFHPFSBQFLLSW-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.77α = 90
b = 47.094β = 94.36
c = 53.951γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Data collection