PDBsum entry 1blx

Complex (inhibitor protein/kinase)

PDB id: 1blx

Contents

Protein chains

305 a.a. *

160 a.a. *

Metals

_CA

Waters ×294

* Residue conservation analysis

PDB id:

1blx

Name:

Complex (inhibitor protein/kinase)

Title:

P19ink4d/cdk6 complex

Structure:

Cyclin-dependent kinase 6. Chain: a. Engineered: yes. P19ink4d. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell_line: sf9. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9. Mus musculus. House mouse.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.200 R-free: 0.253

Authors:

D.H.Brotherton,V.Dhanaraj,S.Wick,L.Brizuela,P.J.Domaille,E.Volyanik, X.Xu,E.Parisini,B.O.Smith,S.J.Archer,M.Serrano,S.L.Brenner, T.L.Blundell,E.D.Laue

Key ref:

D.H.Brotherton et al. (1998). Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d. Nature, 395, 244-250. PubMed id: 9751051 DOI: 10.1038/26164

Date:

21-Jul-98 Release date: 01-Jun-99

Protein chain

Q00534  (CDK6_HUMAN) -  Cyclin-dependent kinase 6 from Homo sapiens

Seq: 326 a.a.

Struc: 305 a.a.

Protein chain

Q60773  (CDN2D_MOUSE) -  Cyclin-dependent kinase 4 inhibitor D from Mus musculus

Seq: 166 a.a.

Struc: 160 a.a.

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.7.11.22 - cyclin-dependent kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺
• Enzyme class 3: Chain B: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/26164

Nature 395:244-250 (1998)

PubMed id: 9751051

Crystal structure of the complex of the cyclin D-dependent kinase Cdk6 bound to the cell-cycle inhibitor p19INK4d.

D.H.Brotherton, V.Dhanaraj, S.Wick, L.Brizuela, P.J.Domaille, E.Volyanik, X.Xu, E.Parisini, B.O.Smith, S.J.Archer, M.Serrano, S.L.Brenner, T.L.Blundell, E.D.Laue.

ABSTRACT

The crystal structure of the cyclin D-dependent kinase Cdk6 bound to the p19 INK4d protein has been determined at 1.9 A resolution. The results provide the first structural information for a cyclin D-dependent protein kinase and show how the INK4 family of CDK inhibitors bind. The structure indicates that the conformational changes induced by p19INK4d inhibit both productive binding of ATP and the cyclin-induced rearrangement of the kinase from an inactive to an active conformation. The structure also shows how binding of an INK4 inhibitor would prevent binding of p27Kip1, resulting in its redistribution to other CDKs. Identification of the critical residues involved in the interaction explains how mutations in Cdk4 and p16INK4a result in loss of kinase inhibition and cancer.

Selected figure(s)

Figure 2.
Figure 2 Three-dimensional structure of the p19^INK4d/Cdk6 complex. a, Stereo view of the C trace of the p19^INK4d/Cdk6 structure. Every tenth C atom is indicated by a solid ball. b, Schematic drawing of the same complex after rotation by 90° about the x axis. c, P19^INK4d and p27^Kip1 prevent each other binding to the CDK subunit in cyclin D/Cdk6. The structure in c is rotated 20° about the z axis compared to b. In a and b p19^INK4d is coloured yellow, apart from helix 3 (residues 46-50), which is red. The C-terminal domain of Cdk6 is coloured light blue, whereas the N-terminal domain, which undergoes extensive movement, is dark blue. In c, p19^INK4d is coloured yellow, Cdk6 is light/dark blue, p27^Kip1 is red and cyclin A is green. p27^Kip1 and cyclin A from the p27^Kip1/cyclin A/Cdk2 structure^40 were superimposed, as described in Fig. 5a, on p19^INK4d/Cdk6 (r.m.s. deviation was 0.46 ? over 70 residues). Figures 2 and 5a, b were produced using the programs MOLSCRIPT47 and RASTER3D^48.

Figure 5.
Figure 5 Comparison of ATP-binding sites in different kinases. a, Comparison of the structure of p19^INK4d/Cdk6 with those of Cdk2 (ref. 15) and Cdk2 from the cyclin A complex16,17. Cdk6 was superimposed on Cdk2 (r.m.s. deviation was 0.56 ? over 70 residues) and Cdk2 from the cyclin A complex (r.m.s. deviation was 0.49 ? over 70 residues) by aligning the C atoms in the -helices in the C-terminal domain of both proteins. Loop L5 and the linker (loop L7) (Fig. 3c), which anchor the N- and C-terminal domains together, are labelled. b, The same structures, showing only the N-terminal domain, illustrating the changes in position of the N-terminal -sheet and helix 1. In both a and b, the N-terminal domains and T-loop are coloured red (Cdk2), yellow (Cdk2 from the cyclin A complex) and blue (Cdk6); other regions of all three proteins are coloured grey. In b, helices 3 and 5 of cyclin A, which interact with PSTAIRE helix 1 in cyclin A/Cdk2 (refs 16, 17), are green. c, The ATP-binding site in Cdk6. Lys 29, His 100 and Asp 102, which together might inhibit ATP binding, are labelled, as are key active-site residues and the phosphate-binding loop L2. ATP, from the active Cdk2/cyclin A complex17, is superimposed on the structure with the N1 and N6 adenine nitrogens making conserved hydrogen bonds with the carbonyl of Glu 99 and amide of Val 101, respectively17,34. The structures of Cdk6 and ATP are yellow and green, respectively. Carbon, nitrogen, oxygen and phosphorus atoms are yellow, blue, red and yellow, respectively. The structure of Cdk2 from the cyclin A/Cdk2 complex17 is blue.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 395, 244-250) copyright 1998.

Figures were selected by the author.