Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme

Abstract

The crystal structure of a fully active form of human protein kinase CK2 (casein kinase 2) consisting of two C-terminally truncated catalytic and two regulatory subunits has been determined at 3.1 A resolution. In the CK2 complex the regulatory subunits form a stable dimer linking the two catalytic subunits, which make no direct contact with one another. Each catalytic subunit interacts with both regulatory chains, predominantly via an extended C-terminal tail of the regulatory subunit. The CK2 structure is consistent with its constitutive activity and with a flexible role of the regulatory subunit as a docking partner for various protein kinases. Furthermore it shows an inter-domain mobility in the catalytic subunit known to be functionally important in protein kinases and detected here for the first time directly within one crystal structure.

Fig. 1. Sequence overview of human CK2α (A) and CK2β (B). Small characters in the sequence indicate residues that are truncated or disordered in both copies of the chains and are therefore left out in the final rhCK2α^Δ structure. Positions at which the final 2F_o – F_c electron density is badly defined are printed in italics. The contact residues are assigned with black bars. The α/β contacts normally occur twice in the rhCK2^Δ complex; if a certain residue was detected as a contact partner only in one chain it is marked with a grey bar instead of a black one. For human A-Raf and Xenopus laevis c-Mos partial sequences are included in (A).

Fig. 2. Electron densities in selected regions of rhCK2^Δ. All maps apart from that covering the AMPPNP molecule in (D) are sigma-weighted 2F_o – F_c electron densities contoured with a 1σ cutoff. The red map in (D) around AMPPNP is an F_o – F_c omit density (4σ cutoff) calculated after a 5000 K simulated annealing run excluding the AMPPNP coordinates. (A) Stereo figure of the CK2β tail as part of the β/β contact. The two rhCK2β subunits are distinguished by different colours (red and blue) for the electron densities and the labels. His165 and Met169 of rhCK2β^Δ (Chantalat et al., 1999) and some corresponding water molecules displaced by the formation of the β/β contact are drawn in black. (B) Stereo figure of the hydrophobic core of the α/β contact. The colour coding for electron densities and labels is black for the CK2β tail with Tyr188 as the central residue of the whole core, red for the body of the second rhCK2β chain and blue for the participating rhCK2α^Δ subunit. (C) The N-terminal segment of rhCK2α^Δ attached to the activation segment (yellow). For comparison the backbone courses of both segments in rmCK2α (Niefind et al., 1999; PDB code: 1DAW) after superimposing on rhCK2α^Δ are drawn in black. Further colour coding for activation segments after three-dimensional fits: red for the partially active CDK2 in complex with a cyclin A fragment (Jeffrey et al., 1995; PDB code: 1FIN) and violet for the inactive CDK2 in isolated form (De Bondt et al., 1993; PDB code: 1HCL). (D) Stereo figure of AMPPNP bound to the active site of rhCK2^Δ chain A1. To compare the γ-phosphate positions, AMPPNP as bound to rmCK2α (Niefind et al., 1999) is drawn in black after superimposition of the protein matrices.

Fig. 3. Various aspects of the rhCK2^Δ structure. (A and B) Overall shape of rhCK2^Δ in a view perpendicular to the local C2 axis (A) and along this axis (B). The two rhCK2β chains are drawn in blue and red, the two rhCK2α^Δ subunits in yellow and grey. (C) Structural overview of rhCK2α^Δ chain A1 with bound AMPPNP and interdomain flexibility. The hinge axis and the bending residues of the domain closure motion as detected by DYNDOM (CCP4, 1994) are included. To illustrate the interdomain flexibility, the N-terminal domains of rmCK2α (PDB code: 1DAW) and of rhCK2α^Δ chain A2 are shown in yellow and black, respectively, after three-dimensional alignment of the corresponding C-terminal domains. (D) Structural overview of rhCK2β. The human CK2β peptide bound to rmCK2α (black) was taken from PDB file: 1DS5 (Battistutta et al., 2000) after superimposition of the corresponding CK2α subunits. (E) Intersubunit flexibility at the α/β contact. Subunit A1 is drawn with yellow colour for the C-terminal domain and grey for the N-terminal domain. Subunit B1 bound to A1 by an α/β contact is sketched in red. Subunit B2 is shown in blue after a three-dimensional fit of the N-terminal domain of subunit A2 (not drawn) on that of A1.

Fig. 4. Electrostatic surface of rhCK2^Δ. The surface is coloured according to the electrostatic potential ranging from deep blue (positive charge) to red (negative charge). Atomic charges were assigned by GRASP (Nicholls et al., 1991) using default values.