Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.83 kDa 
• Atom Count: 1698 
• Modelled Residue Count: 171 
• Deposited Residue Count: 175 
• Unique protein chains: 1

2A2K

Crystal Structure of an active site mutant, C473S, of Cdc25B Phosphatase Catalytic Domain

• PDB DOI: 10.2210/pdb2A2K/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-06-22 Released: 2006-01-03 
• Deposition Author(s): Sohn, J., Parks, J., Buhrman, G., Brown, P., Kristjansdottir, K., Safi, A., Yang, W., Edelsbrunner, H., Rudolph, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.191 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.

Sohn, J., Parks, J.M., Buhrman, G., Brown, P., Safi, A., Edelsbrunner, H., Yang, W., Rudolph, J.

(2005) Biochemistry 44: 16563-16573

• PubMed: 16342947 
• DOI: 10.1021/bi0516879
• Primary Citation of Related Structures:  
  2A2K


• PubMed 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.

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Organizational Affiliation: 

Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M-phase inducer phosphatase 2	A	175	Homo sapiens	Mutation(s): 1  Gene Names: CDC25B, CDC25HU2 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P30305 (Homo sapiens) Explore P30305  Go to UniProtKB:  P30305
PHAROS:  P30305

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.191 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.247	α = 90
b = 70.933	β = 90
c = 74.056	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-22 
• Released Date: 2006-01-03 
Deposition Author(s): Sohn, J., Parks, J., Buhrman, G., Brown, P., Kristjansdottir, K., Safi, A., Yang, W., Edelsbrunner, H., Rudolph, J.

Revision History  

• Version 1.0: 2006-01-03
  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: 2021-10-20
  Changes: Database references, Derived calculations