2CCH

The crystal structure of CDK2 cyclin A in complex with a substrate peptide derived from CDC modified with a gamma-linked ATP analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Role of the Phospho-Cdk2/Cyclin a Recruitment Site in Substrate Recognition

Cheng, K.Y.Noble, M.E.M.Skamnaki, V.Brown, N.R.Lowe, E.D.Kontogiannis, L.Shen, K.Cole, P.A.Siligardi, G.Johnson, L.N.

(2006) J Biol Chem 281: 23167

  • DOI: 10.1074/jbc.M600480200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the catalytic site. The role of this recruitment site, which enhances substrate affinity and catalytic efficiency, ...

    Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the catalytic site. The role of this recruitment site, which enhances substrate affinity and catalytic efficiency, has been investigated using peptides derived from the natural substrates, namely CDC6 and p107, and a bispeptide inhibitor in which the gamma-phosphate of ATP is covalently attached by a linker to the CDC6 substrate peptide. X-ray studies with a 30-residue CDC6 peptide in complex with pCDK2/cyclin A showed binding of a dodecamer peptide at the recruitment site and a heptapeptide at the catalytic site, but no density for the linking 11 residues. Kinetic studies established that the CDC6 peptide had an 18-fold lower Km compared with heptapeptide substrate and that this effect required the recruitment peptide to be covalently linked to the substrate peptide. X-ray studies with the CDC6 bispeptide showed binding of the dodecamer at the recruitment site and the modified ATP in two alternative conformations at the catalytic site. The CDC6 bispeptide was a potent inhibitor competitive with both ATP and peptide substrate of pCDK2/cyclin A activity against a heptapeptide substrate (Ki = 0.83 nm) but less effective against RXL-containing substrates. We discuss how localization at the recruitment site (KD 0.4 microm) leads to increased catalytic efficiency and the design of a potent inhibitor. The notion of a flexible linker between the sites, which must have more than a minimal number of residues, provides an explanation for recognition and discrimination against different substrates.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A, C
299Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.1 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLIN A2
B, D
260Homo sapiensMutation(s): 0 
Gene Names: CCNA2CCN1CCNA
Find proteins for P20248 (Homo sapiens)
Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS  P20248
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
E, F
12Homo sapiensMutation(s): 0 
Gene Names: CDC6CDC18L
Find proteins for Q99741 (Homo sapiens)
Go to UniProtKB:  Q99741
NIH Common Fund Data Resources
PHAROS  Q99741
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A,CL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.535α = 90
b = 114.483β = 90
c = 181.299γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-02-27
    Changes: Data collection, Derived calculations, Experimental preparation, Other