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PDBsum entry 4i3z

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protein ligands metals links
Transferase/cell cycle PDB id
4i3z
Jmol
Contents
Protein chains
296 a.a.
257 a.a.
Ligands
ADP ×2
GOL ×9
Metals
_CL ×2
_MG ×4
Waters ×521
PDB id:
4i3z
Name: Transferase/cell cycle
Title: Structure of pcdk2/cyclina bound to adp and 2 magnesium ions
Structure: Cyclin-dependent kinase 2. Chain: a, c. Synonym: cell division protein kinase 2, p33 protein kinase engineered: yes. Cyclin-a2. Chain: b, d. Fragment: unp residues 105-421. Synonym: cyclin-a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cdk2, cdkn2. Expressed in: escherichia coli. Expression_system_taxid: 511693. Mus musculus. Mouse. Organism_taxid: 10090.
Resolution:
2.05Å     R-factor:   0.199     R-free:   0.228
Authors: D.M.Jacobsen,Z.-Q.Bao,P.J.O'Brien,C.L.Brooks,M.A.Young
Key ref: D.M.Jacobsen et al. (2012). Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase. J Am Chem Soc, 134, 15357-15370. PubMed id: 22891849
Date:
27-Nov-12     Release date:   26-Dec-12    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2
Seq:
Struc:
298 a.a.
296 a.a.*
Protein chains
Pfam   ArchSchema ?
P51943  (CCNA2_MOUSE) -  Cyclin-A2
Seq:
Struc:
422 a.a.
257 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, C: E.C.2.7.11.22  - Cyclin-dependent kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + a protein = ADP + a phosphoprotein
ATP
+ protein
= ADP
+ phosphoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cyclin-dependent protein kinase holoenzyme complex   15 terms 
  Biological process     regulation of gene silencing   30 terms 
  Biochemical function     nucleotide binding     13 terms  

 

 
    reference    
 
 
J Am Chem Soc 134:15357-15370 (2012)
PubMed id: 22891849  
 
 
Price to be paid for two-metal catalysis: magnesium ions that accelerate chemistry unavoidably limit product release from a protein kinase.
D.M.Jacobsen, Z.Q.Bao, P.O'Brien, C.L.Brooks, M.A.Young.
 
  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 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.