4I3Z

Structure of pCDK2/CyclinA bound to ADP and 2 Magnesium ions

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


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Literature

Price To Be Paid for Two-Metal Catalysis: Magnesium Ions That Accelerate Chemistry Unavoidably Limit Product Release from a Protein Kinase

Jacobsen, D.M., Bao, Z.-Q., O'Brien, P.J., Brooks, C.L., Young, M.A.

(2012) J Am Chem Soc 134: 15357-15370

  • DOI: 10.1021/ja304419t
  • Primary Citation of Related Structures:  
    4I3Z, 4II5

  • PubMed Abstract: 

    • Incorporation of divalent metal ions into an active site is a fundamental catalytic tool used by diverse enzymes. Divalent cations are used by protein kinases to both stabilize ATP binding and accelerate chemistry. Kinetic analysis establishes that Cycli ...

    Incorporation of divalent metal ions into an active site is a fundamental catalytic tool used by diverse enzymes. Divalent cations are used by protein kinases to both stabilize ATP binding and accelerate chemistry. Kinetic analysis establishes that Cyclin-dependent kinase 2 (CDK2) requires simultaneous binding of two Mg(2+) ions for catalysis of phosphoryl transfer. This tool, however, comes with a price: the rate-acceleration effects are opposed by an unavoidable rate-limiting consequence of the use of two Mg(2+) ions by CDK2. The essential metal ions stabilize ADP product binding and limit the overall rate of the reaction. We demonstrate that product release is rate limiting for activated CDK2 and evaluate the effects of the two catalytically essential Mg(2+) ions on the stability of the ADP product within the active site. We present two new crystal structures of CDK2 bound to ADP showing how the phosphate groups can be coordinated by either one or two Mg(2+) ions, with the occupancy of one site in a weaker equilibrium. Molecular dynamics simulations indicate that ADP phosphate mobility is more restricted when ADP is coordinated by two Mg(2+) ions compared to one. The structural similarity between the rigid ADP·2Mg product and the cooperatively assembled transition state provides a mechanistic rational for the rate-limiting ADP release that is observed. We demonstrate that although the simultaneous binding of two Mg(2+) ions is essential for efficient phosphoryl transfer, the presence of both Mg(2+) ions in the active site also cooperatively increases ADP affinity and opposes its release. Evolution of protein kinases must have involved careful tuning of the affinity for the second Mg(2+) ion in order to balance the needs to stabilize the chemical transition state and allow timely product release. The link between Mg(2+) site affinity and activity presents a chemical handle that may be used by regulatory factors as well as explain some mutational effects.

    Organizational Affiliation: 

    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 2 A, C296Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS:  P24941
GTEx:  ENSG00000123374
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-A2 B, D257Mus musculusMutation(s): 0 
Gene Names: Ccna, Ccna2, Cyca, Cyca2
Find proteins for P51943 (Mus musculus)
Explore P51943 
Go to UniProtKB:  P51943
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		A,CL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKd :  51300   nM  PDBBind
ADPKd:  51300000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.77α = 90
b = 164.13β = 107.07
c = 73.28γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description