PDBsum entry 1t3k

Go to PDB code: 
protein metals links
Hydrolase PDB id
Protein chain
132 a.a. *
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Nmr structure of a cdc25-like dual-specificity tyrosine phosphatase of arabidopsis thaliana
Structure: Dual-specificity tyrosine phosphatase. Chain: a. Synonym: arath cdc25. Engineered: yes. Mutation: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: cdc25. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: I.Landrieu,M.Da Costa,L.De Veylder,F.Dewitte,K.Vandepoele, S.Hassan,J.M.Wieruszeski,J.D.Faure,D.Inze,G.Lippens
Key ref:
I.Landrieu et al. (2004). A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana. Proc Natl Acad Sci U S A, 101, 13380-13385. PubMed id: 15329414 DOI: 10.1073/pnas.0405248101
27-Apr-04     Release date:   07-Sep-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8GY31  (CDC25_ARATH) -  Dual specificity phosphatase Cdc25
146 a.a.
132 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
= protein tyrosine
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   3 terms 
  Biological process     peptidyl-tyrosine dephosphorylation   8 terms 
  Biochemical function     protein binding     7 terms  


DOI no: 10.1073/pnas.0405248101 Proc Natl Acad Sci U S A 101:13380-13385 (2004)
PubMed id: 15329414  
A small CDC25 dual-specificity tyrosine-phosphatase isoform in Arabidopsis thaliana.
I.Landrieu, M.da Costa, L.De Veylder, F.Dewitte, K.Vandepoele, S.Hassan, J.M.Wieruszeski, F.Corellou, J.D.Faure, M.Van Montagu, D.Inzé, G.Lippens.
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.
  Selected figure(s)  
Figure 1.
Fig. 1. Sequence comparison of the Arath;CDC25 protein with CDC25, small CDC25-like tyrosine phosphatases, and the yeast arsenate reductase ACR2. Identical amino acids in all of the sequences are shown in white on a black background. Conserved amino acids are in bold. Secondary structure elements are indicated above the alignment for human CDC25A (PDB ID 1C25 [PDB] ) and below for A. thaliana Arath;CDC25. The catalytic loop is indicated by the HC(X)[5]R motif. CDC25ACDC25A_human, human CDC25A (accession number NP_001780 [GenBank] ); CDC25B_human, human CDC25B (NP_068658 [GenBank] ); CDC25C_human, human CDC25C (NP_073720 [GenBank] ); CDC25_pombe, Sch. pombe CDC25 (NP_013750 [GenBank] ); MIH1_cerevisiae, S. cerevisiae CDC25 (NP_013750 [GenBank] ); YGR203_cerevisiae, S. cerevisiae protein of unknown function (NP_011719 [GenBank] ); ACR2_cerevisiae, S. cerevisiae arsenate reductase (NP_015526 [GenBank] ); IBP1_pombe, Sch. pombe small CDC25-like protein (AL096796 [GenBank] ); Orysa;CDC25;1, O. sativa protein of unknown function (NP_922597 [GenBank] ); Arath;CDC25_Arabidop, this work (NP_568119 [GenBank] ).
Figure 3.
Fig. 3. Ribbon representation in the same orientation of the backbone of a representative conformer of the Arath;CDC25 protein (Left) and the human CDC25A (Right) (PDB entry 1C25 [PDB] , ref. 4). The conserved five-stranded -sheet and 4 helices of the structures have been superposed as described in Results. The catalytic loop is indicated by the HC(X)[5]R motif. The zinc ion is represented as a black sphere.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21199834 C.Chevalier, M.Nafati, E.Mathieu-Rivet, M.Bourdon, N.Frangne, C.Cheniclet, J.P.Renaudin, F.Gévaudant, and M.Hernould (2011).
Elucidating the functional role of endoreduplication in tomato fruit development.
  Ann Bot, 107, 1159-1169.  
21558458 D.Francis (2011).
A commentary on the G2/M transition of the plant cell cycle.
  Ann Bot, 107, 1065-1070.  
21339187 H.Lipavská, P.Masková, and P.Vojvodová (2011).
Regulatory dephosphorylation of CDK at G2/M in plants: yeast mitotic phosphatase cdc25 induces cytokinin-like effects in transgenic tobacco morphogenesis.
  Ann Bot, 107, 1071-1086.  
20135153 J.Papenbrock, S.Guretzki, and M.Henne (2011).
Latest news about the sulfurtransferase protein family of higher plants.
  Amino Acids, 41, 43-57.  
19341304 A.L.Skinner, A.A.Vartia, T.D.Williams, and J.S.Laurence (2009).
Enzyme activity of phosphatase of regenerating liver is controlled by the redox environment and its C-terminal residues.
  Biochemistry, 48, 4262-4272.  
19392699 J.d.e. .A.Engler, L.De Veylder, R.De Groodt, S.Rombauts, V.Boudolf, B.De Meyer, A.Hemerly, P.Ferreira, T.Beeckman, M.Karimi, P.Hilson, D.Inzé, and G.Engler (2009).
Systematic analysis of cell-cycle gene expression during Arabidopsis development.
  Plant J, 59, 645-660.  
17333251 A.Hussain, D.Cao, and J.Peng (2007).
Identification of conserved tyrosine residues important for gibberellin sensitivity of Arabidopsis RGL2 protein.
  Planta, 226, 475-483.  
17388890 D.Francis (2007).
The plant cell cycle--15 years on.
  New Phytol, 174, 261-278.  
17388894 G.L.Duan, Y.Zhou, Y.P.Tong, R.Mukhopadhyay, B.P.Rosen, and Y.G.Zhu (2007).
A CDC25 homologue from rice functions as an arsenate reductase.
  New Phytol, 174, 311-321.  
17443687 L.Sun, Y.Chai, R.Hannigan, V.K.Bhogaraju, and K.Machaca (2007).
Zinc regulates the ability of Cdc25C to activate MPF/cdk1.
  J Cell Physiol, 213, 98.  
17587306 N.Gonzalez, F.Gévaudant, M.Hernould, C.Chevalier, and A.Mouras (2007).
The cell cycle-associated protein kinase WEE1 regulates cell size in relation to endoreduplication in developing tomato fruit.
  Plant J, 51, 642-655.  
16429264 B.Farinas, C.Mary, O Manes, Y.Bhaud, G.Peaucellier, and H.Moreau (2006).
Natural synchronisation for the study of cell division in the green unicellular alga Ostreococcus tauri.
  Plant Mol Biol, 60, 277-292.  
16724265 D.Francis, and N.G.Halford (2006).
Nutrient sensing in plant meristems.
  Plant Mol Biol, 60, 981-993.  
17094738 D.Inzé, and L.De Veylder (2006).
Cell cycle regulation in plant development.
  Annu Rev Genet, 40, 77.  
16885238 J.M.Yang, and C.H.Tung (2006).
Protein structure database search and evolutionary classification.
  Nucleic Acids Res, 34, 3646-3659.  
16567632 O.P.Dhankher, B.P.Rosen, E.C.McKinney, and R.B.Meagher (2006).
Hyperaccumulation of arsenic in the shoots of Arabidopsis silenced for arsenate reductase (ACR2).
  Proc Natl Acad Sci U S A, 103, 5413-5418.  
16724263 V.C.Gegas, and J.H.Doonan (2006).
Expression of cell cycle genes in shoot apical meristems.
  Plant Mol Biol, 60, 947-961.  
16212607 C.B.Orchard, I.Siciliano, D.A.Sorrell, A.Marchbank, H.J.Rogers, D.Francis, R.J.Herbert, P.Suchomelova, H.Lipavska, A.Azmi, and H.Van Onckelen (2005).
Tobacco BY-2 cells expressing fission yeast cdc25 bypass a G2/M block on the cell cycle.
  Plant J, 44, 290-299.  
15720653 D.A.Sorrell, D.Chrimes, J.R.Dickinson, H.J.Rogers, and D.Francis (2005).
The Arabidopsis CDC25 induces a short cell length when overexpressed in fission yeast: evidence for cell cycle function.
  New Phytol, 165, 425-428.  
15760362 D.Chrimes, H.J.Rogers, D.Francis, H.D.Jones, and C.Ainsworth (2005).
Expression of fission yeast cdc25 driven by the wheat ADP-glucose pyrophosphorylase large subunit promoter reduces pollen viability and prevents transmission of the transgene in wheat.
  New Phytol, 166, 185-192.  
15678103 D.Inzé (2005).
Green light for the cell cycle.
  EMBO J, 24, 657-662.  
15686519 M.Menges, Jager, W.Gruissem, and J.A.Murray (2005).
Global analysis of the core cell cycle regulators of Arabidopsis identifies novel genes, reveals multiple and highly specific profiles of expression and provides a coherent model for plant cell cycle control.
  Plant J, 41, 546-566.  
16212609 W.G.Brenner, G.A.Romanov, I.Köllmer, L.Bürkle, and T.Schmülling (2005).
Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades.
  Plant J, 44, 314-333.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.