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 1T3K | pdb_00001t3k

NMR structure of a CDC25-like dual-specificity tyrosine phosphatase of Arabidopsis thaliana


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

Validation slider image for 1T3K

This is version 1.4 of the entry. See complete history. 

Literature

A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana.

Landrieu, I., Da Costa, M., De Veylder, L., Dewitte, F., Vandepoele, K., Hassan, S., Wieruszeski, J.M., Faure, J.D., Van Montagu, M., Inze, D., Lippens, G.

(2004) Proc Natl Acad Sci U S A 101: 13380-13385

  • DOI: https://doi.org/10.1073/pnas.0405248101
  • Primary Citation Related Structures: 
    1T3K

  • PubMed Abstract: 

    The dual-specificity CDC25 phosphatases are critical positive regulators of cyclin-dependent kinases (CDKs). Even though an antagonistic Arabidopsis thaliana WEE1 kinase has been cloned and tyrosine phosphorylation of its CDKs has been demonstrated, no valid candidate for a CDC25 protein has been reported in higher plants. We identify a CDC25-related protein (Arath;CDC25) of A. thaliana, constituted by a sole catalytic domain. The protein has a tyrosine-phosphatase activity and stimulates the kinase activity of Arabidopsis CDKs. Its tertiary structure was obtained by NMR spectroscopy and confirms that Arath;CDC25 belongs structurally to the classical CDC25 superfamily with a central five-stranded beta-sheet surrounded by helices. A particular feature of the protein, however, is the presence of an additional zinc-binding loop in the C-terminal part. NMR mapping studies revealed the interaction with phosphorylated peptidic models derived from the conserved CDK loop containing the phosphothreonine-14 and phosphotyrosine-15. We conclude that despite sequence divergence, Arath;CDC25 is structurally and functionally an isoform of the CDC25 superfamily, which is conserved in yeast and in plants, including Arabidopsis and rice.


  • Organizational Affiliation: 
    • Unité Mixte de Recherche 8525 Centre National de la Recherche Scientifique-Lille2, Institut de Biologie de Lille/Pasteur Institute of Lille, 59019 Lille Cedex, France. isabelle.landrieu@ibl.fr

Macromolecule Content 

  • Total Structure Weight: 17.01 kDa 
  • Atom Count: 1,033 
  • Modeled Residue Count: 132 
  • Deposited Residue Count: 152 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual-specificity tyrosine phosphatase152Arabidopsis thalianaMutation(s): 1 
Gene Names: CDC25
EC: 3.1.3.48 (PDB Primary Data), 1.20.4.1 (UniProt)
UniProt
Find proteins for Q8GY31 (Arabidopsis thaliana)
Explore Q8GY31 
Go to UniProtKB:  Q8GY31
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GY31
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection