4WDG

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, with mutation V321A, complexed with 2',5'-ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.241 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/srep16520
  • Primary Citation of Related Structures:  
    4WBI, 4WBL, 4WC9, 4WCA, 4WCB, 4WCC, 4WDA, 4WDB, 4WDD, 4WDE, 4WDF, 4WDG, 4WDH, 4WEX, 4WFR, 5AE0

  • 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 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

    Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2',3'-cyclic-nucleotide 3'-phosphodiesterase221Mus musculusMutation(s): 1 
Gene Names: CnpCnp1
EC: 3.1.4.37
UniProt & NIH Common Fund Data Resources
Find proteins for P16330 (Mus musculus)
Explore P16330 
Go to UniProtKB:  P16330
IMPC:  MGI:88437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16330
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2P
Query on A2P

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-2'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
AEOBEOJCBAYXBA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.33α = 90
b = 46.94β = 90
c = 106.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description