PDBsum entry 1buh

Transferase

PDB id: 1buh

Contents

Protein chains

287 a.a. *

70 a.a. *

Waters ×127

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure and mutational analysis of the human cdk2 kinase complex with cell cycle-Regulatory protein ckshs1.

Authors

Y.Bourne, M.H.Watson, M.J.Hickey, W.Holmes, W.Rocque, S.I.Reed, J.A.Tainer.

Ref.

Cell, 1996, 84, 863-874. [DOI no: 10.1016/S0092-8674(00)81065-X]

PubMed id

8601310

Abstract

The 2.6 Angstrom crystal structure for human cyclin-dependent kinase 2(CDK2) in complex with CksHs1, a human homolog of essential yeast cell cycle-regulatory proteins suc1 and Cks1, reveals that CksHs1 binds via all four beta strands to the kinase C-terminal lobe. This interface is biologically critical, based upon mutational analysis, but far from the CDK2 N-terminal lobe, cyclin, and regulatory phosphorylation sites. CDK2 binds the Cks single domain conformation and interacts with conserved hydrophobic residues plus His-60 and Glu-63 in their closed beta-hinge motif conformation. The beta hinge opening to form the Cks beta-interchanged dimer sterically precludes CDK2 binding, providing a possible mechanism regulating CDK2-Cks interactions. One face of the complex exposes the sequence-conserved phosphate-binding region on Cks and the ATP-binding site on CDK2, suggesting that CKs may target CDK2 to other phosphoproteins during the cell cycle.

Figure 1.
Figure 1. Quality of the Structure and Overall View of the CDK2–CksHs1 Complex(A) Stereo view of the 2.6 Å resolution omit Fo–Fc electron density map, contoured at 2σ, showing the predominant cluster of hydrophobic residues forming the binding interface. The coordinates of this region (5% of the total number of atoms) were omitted and the protein coordinates were refined by simulated annealing before the phase calculation. Residues are labeled in white for CDK2 and in yellow for CksHs1.(B) Ribbon diagram of CksHs1 (yellow) bound to CDK2, with the N-lobe in purple and the C-lobe in blue and green. The ATP molecule is displayed at the interface of the two CDK2 lobes (white bonds with red oxygen and blue nitrogen atoms as spheres) and is taken from the free CDK2 coordinates ([11]). The functional structural elements are color coded for CDK2: the β1–β2 loop, red; the disordered loop to the PSTAIRE sequence in helix α1, asterisks; the T loop, white. Side chains forming the phosphorylation sites in the β1–β2 loop (Thr-14 and Tyr-15) and in the T loop (Thr-160) (orange bonds with red oxygen atoms as balls), as well as the CksHs1 side chains forming the conserved phosphate anion–binding site (β1 Lys-11, β2 Arg-20, β3 Trp-54, and β4 Arg-71) (white bonds with blue nitrogen atoms as balls), are displayed. The CDK2 secondary elements involved in the binding interface are highlighted (green), and CksHs1 loops β1–β2 and β3–β4 are labeled L1 and L3, respectively.(C) CksHs1 molecular surface, colored with the residues buried to a 1.6 Å probe radius in pale yellow, the nonburied residues in white, and the phosphate anion–binding site in blue. A ribbon diagram of the CDK2 molecule is shown with the color code and orientation as in (B). A CksHs1 Cα trace (orange) is shown through the surface and reveals that the buried residues cluster in the interior concave face of the CksHs1 β sheet and in the β1–β2 and β3–β4 loops, which envelop the CDK2 helix α5 and loop L14 (green).(D) CDK2 molecular surface, with buried residues in helix α5 (green) and loop L14 (cyan); nonburied residues are shown in white. CksHs1 residues involved in the binding interface are shown (orange bonds with red oxygen, blue nitrogen, and yellow sulfur atoms as balls) with a Cα trace (yellow). CksHs1 residues in all four β strands participate in the binding interface.

Figure 5.
Figure 5. The CDK2–Cyclin A–CksHs1 Ternary Complex(A) Ribbon diagram of a CDK2–cyclin A–CksHs1 complex model based on the coordinates of our CDK2–CksHs1 complex and those of a CDK2–cyclin A complex ([30]) in which the two CDK2 molecules were superimposed based on the Cα atoms of the C-lobe. Besides two distinct binding sites for cyclin A and CksHs1 at the molecular surface of CDK2, this model reveals a large bowl-shaped groove centered around the phosphorylation site at Thr-160 (middle) in the activated conformation of the CDK2 T loop and bordered by cyclin A and CksHs1 molecules. The presence of positively charged residues (Lys-24, Lys-30, and Lys-34 in CksHs1 and Lys-226 and Lys-417 in cyclin A) located on each side of the groove is displayed (purple bonds and blue for nitrogen atoms as balls). The molecules and the functionally important elements in CDK2 are color coded as in Figure 1B, with cyclin A in green. ATP is taken from the CDK2–cyclin A complex coordinates previously described ( [30]).(B) Molecular surface of the CDK2–cyclin A–CksHs1 complex oriented vert, similar 90° away from that in (A), with the same color code. The CksHs1 phosphate anion–binding site (blue) is exposed into the solvent and located on the same side of the CDK2 catalytic site with the ATP molecule bound between the two lobes, thus forming a continuous surface for recognition of a Cdk substrate or other phosphoproteins. The two CksHs1 α helices (orange) are also solvent accessible. The T loop (white), containing the phosphorylation site at position Thr-160 (middle), protrudes at the interface of CksHs1 and cyclin A. Figure 1 and Figure 2 and 2B, 3C, and 4 were generated with the Application Visualization System (AVS) (Advanced Visual Systems, Waltham, Massachusetts), and Figure 1A and Figure 2C were generated with TURBO-FRODO ( [52]). The solvent-accessible surfaces were calculated with MS ( [9]), and the ribbon diagrams were generated using RIBBONS ( [8]) implemented in AVS.

The above figures are reprinted by permission from Cell Press: Cell (1996, 84, 863-874) copyright 1996.