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PDBsum entry 2a2k

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protein ligands metals links
Hydrolase PDB id
2a2k
Jmol
Contents
Protein chain
171 a.a. *
Ligands
SO4
Metals
_CL ×2
Waters ×219
* Residue conservation analysis
PDB id:
2a2k
Name: Hydrolase
Title: Crystal structure of an active site mutant, c473s, of cdc25b phosphatase catalytic domain
Structure: M-phase inducer phosphatase 2. Chain: a. Fragment: catalytic domain. Synonym: dual specificity phosphatase cdc25b. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cdc25b, cdc25hu2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
1.52Å     R-factor:   0.182     R-free:   0.191
Authors: J.Sohn,J.Parks,G.Buhrman,P.Brown,K.Kristjansdottir,A.Safi, W.Yang,H.Edelsbrunner,J.Rudolph
Key ref:
J.Sohn et al. (2005). Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry, 44, 16563-16573. PubMed id: 16342947 DOI: 10.1021/bi0516879
Date:
22-Jun-05     Release date:   03-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P30305  (MPIP2_HUMAN) -  M-phase inducer phosphatase 2
Seq:
Struc:
 
Seq:
Struc:
580 a.a.
171 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.48  - 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     intracellular   1 term 
  Biological process     M phase of mitotic cell cycle   2 terms 
  Biochemical function     protein tyrosine phosphatase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1021/bi0516879 Biochemistry 44:16563-16573 (2005)
PubMed id: 16342947  
 
 
Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate.
J.Sohn, J.M.Parks, G.Buhrman, P.Brown, K.Kristjánsdóttir, A.Safi, H.Edelsbrunner, W.Yang, J.Rudolph.
 
  ABSTRACT  
 
Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling anticancer targets because their overexpression has been associated with numerous cancers. However, drug discovery targeting these phosphatases has been hampered by the lack of structural information about how Cdc25s interact with their native protein substrates, the cyclin-dependent kinases. Herein, we predict a docked orientation for Cdc25B with its Cdk2-pTpY-CycA protein substrate by a rigid-body docking method and refine the docked models with full-scale molecular dynamics simulations and minimization. We validate the stable ensemble structure experimentally by a variety of in vitro and in vivo techniques. Specifically, we compare our model with a crystal structure of the substrate-trapping mutant of Cdc25B. We identify and validate in vivo a novel hot-spot residue on Cdc25B (Arg492) that plays a central role in protein substrate recognition. We identify a hot-spot residue on the substrate Cdk2 (Asp206) and confirm its interaction with hot-spot residues on Cdc25 using hot-spot swapping and double mutant cycles to derive interaction energies. Our experimentally validated model is consistent with previous studies of Cdk2 and its interaction partners and initiates the opportunity for drug discovery of inhibitors that target the remote binding sites of this protein-protein interaction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21329431 M.Radulovic, and J.Godovac-Zimmermann (2011).
Proteomic approaches to understanding the role of the cytoskeleton in host-defense mechanisms.
  Expert Rev Proteomics, 8, 117-126.  
20740493 G.M.Arantes (2010).
Flexibility and inhibitor binding in cdc25 phosphatases.
  Proteins, 78, 3017-3032.  
19301836 J.M.Parks, H.Hu, J.Rudolph, and W.Yang (2009).
Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations.
  J Phys Chem B, 113, 5217-5224.  
19530895 P.A.Johnston, C.A.Foster, M.B.Tierno, T.Y.Shun, S.N.Shinde, W.D.Paquette, K.M.Brummond, P.Wipf, and J.S.Lazo (2009).
Cdc25B dual-specificity phosphatase inhibitors identified in a high-throughput screen of the NIH compound library.
  Assay Drug Dev Technol, 7, 250-265.  
19028102 S.Cao, B.T.Murphy, C.Foster, J.S.Lazo, and D.G.Kingston (2009).
Bioactivities of simplified adociaquinone B and naphthoquinone derivatives against Cdc25B, MKP-1, and MKP-3 phosphatases.
  Bioorg Med Chem, 17, 2276-2281.  
18855677 A.Bakan, J.S.Lazo, P.Wipf, K.M.Brummond, and I.Bahar (2008).
Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening.
  Curr Med Chem, 15, 2536-2544.  
17239579 D.Reichmann, O.Rahat, M.Cohen, H.Neuvirth, and G.Schreiber (2007).
The molecular architecture of protein-protein binding sites.
  Curr Opin Struct Biol, 17, 67-76.  
17298081 F.Naider, J.M.Becker, Y.H.Lee, and A.Horovitz (2007).
Double-mutant cycle scanning of the interaction of a peptide ligand and its G protein-coupled receptor.
  Biochemistry, 46, 3476-3481.  
17287826 J.Rudolph (2007).
Inhibiting transient protein-protein interactions: lessons from the Cdc25 protein tyrosine phosphatases.
  Nat Rev Cancer, 7, 202-211.  
17174465 J.Sohn, and J.Rudolph (2007).
Temperature dependence of binding and catalysis for the Cdc25B phosphatase.
  Biophys Chem, 125, 549-555.  
16950393 J.Sohn, and J.Rudolph (2006).
The energetic network of hotspot residues between Cdc25B phosphatase and its protein substrate.
  J Mol Biol, 362, 1060-1071.  
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.