Crystal structure of human CDK4 in complex with a D-type cyclin

Abstract

The cyclin D1-cyclin-dependent kinase 4 (CDK4) complex is a key regulator of the transition through the G1 phase of the cell cycle. Among the cyclin/CDKs, CDK4 and cyclin D1 are the most frequently activated by somatic genetic alterations in multiple tumor types. Thus, aberrant regulation of the CDK4/cyclin D1 pathway plays an essential role in oncogenesis; hence, CDK4 is a genetically validated therapeutic target. Although X-ray crystallographic structures have been determined for various CDK/cyclin complexes, CDK4/cyclin D1 has remained highly refractory to structure determination. Here, we report the crystal structure of CDK4 in complex with cyclin D1 at a resolution of 2.3 Å. Although CDK4 is bound to cyclin D1 and has a phosphorylated T-loop, CDK4 is in an inactive conformation and the conformation of the heterodimer diverges from the previously known CDK/cyclin binary complexes, which suggests a unique mechanism for the process of CDK4 regulation and activation. CDK4 and CDK6 associate with the D-type cyclins (D1, D2, D3) and phosphorylate and inactivate the retinoblastoma (Rb) protein family members (p107, p130, pRb). Phosphorylation of pRb by CDK4/6 then leads to the derepression and activation of E2F target genes, including the E-type cyclins, which facilitate progression through the G 1 phase of the cell cycle.Deregulation of the CDK4/cyclin D pathway has been identified in many cancers (refs. 4 and 5 and references therein and ref. 6). Notably, most genetic alterations target specifically CDK4 or cyclin D1, whereas alterations in other CDKs and cyclins are far less common. The CDK4 gene is amplified in a high percentage of liposarcomas (7), and breast cancers frequently exhibit high cyclin D1 levels, either through genetic amplification of the gene or overexpression (8). Translocation of cyclin D1 to the IgH promoter is a hallmark aberration in mantle cell lymphoma (9). Cyclin D1 translocations can also be detected in many cases of multiple myelomas (10). A mutation of CDK4 (Arg-24-Cys) that renders it refractory to inhibition by the tumor suppressor protein p16INK4a has also been identified, and, similarly, deletion or mutation of the p16INK4a gene results in defective CDK4 inhibition and dysregulated CDK4 activity (11). Finally, genetic inactivation of p16INK4 is among the most frequent tumor suppressor mutations found in human cancers. Taken together, these data indicate that an unchecked or hyperactivated CDK4/cyclin D1 pathway may be responsible for enhanced cellular proliferation in cancers and imply that CDK4 is a promising target for the development of anticancer therapies (reviewed in ref. 12).The molecular basis of CDK activation has been the focus of many studies using cellular, biochemical, and structural approaches (reviewed in ref.3). Maximal CDK activation requires both binding of a cognate cyclin and phosphorylation of residues within the CDK T-loop, and X-ray crystallographic studies of various CDKs and CDK/cyclin complexes have identified the conformational movements associated with ...

Targeting CDK6 in cancer: State of the art and new insights

“…Furthermore, there are several 3.10 1JOW CDK6 -Vcyclin -9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido [4,5]pyrrolo[1,2-d]pyrimidin-2-amine 109 2.90 4TTH CDK6 -Vcyclin -Aminopurvalanol 114 2.80 2F2C CDK6 -Vcyclin -Fisetin 117 2.90 1XO2 CDK6 -Vcyclin -PD0332991 114 3.00 2EUF CDK6 -Kcyclin -p18 INK4c 118 2 111 2.70 4EZ5 CDK6 -1H-benzimidazol-2-yl(1H-pyrrol-2-yl)methanone 111 2.31 4AUA CDK6 -4-[3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(1-methylpiperidin-4-yl)pyrimidin-2-amine 119 2.60 3NUP CDK6 -4-[5-chloro-3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(5-piperazin-1-ylpyridin-2-yl)pyrimidin-2-amine 119 2.70 3NUX CDK6 -p16 INK4a 83 3.40 1BI7 CDK6 -p19 INK4d 74,83 1.90 1BLX 2.80 1BI8 lines of evidence showing that CDK4 might not even be phosphorylated by CAK. 77,78 The INK4 family of CDK inhibitors (CDKIs) which include p16 INK4a , p15 INK4b , p18 INK4c , and p19 INK4d are specific to CDK4 and CDK6. They bind to either the monomeric CDK or the CDK-cyclin D complex resulting in inactivation of the enzyme.…”

Cyclin-Cyclin-dependent Kinase Regulatory Response Is Linked to Substrate Recognition

“…INK4 binding has far reaching impacts on the CDK catalytic core, including distorting the ␣1/PSTAIRE helix and the T loop (15), and CAK phosphorylation affects positioning of the T loop, raising the possibility that the resistance to these regulatory influences may be achieved through directly or indirectly affecting the conformation of these structural elements. Two recently published structures of CDK4 in complex with cellular D-cyclins (62,63) reveal considerable involvement of CL-B residues in the interface between the cyclin D and the CDK N-lobe that is far more pronounced in these than in other cyclin-CDK complexes. In fact, in the herpesvirus saimiri D cyclin-CDK6 complex, these residues remain near fully solvent-accessible, effectively reducing the interface contact to the CDK.…”

7,3′,4′-Trihydroxyisoflavone Inhibits Epidermal Growth Factor-induced Proliferation and Transformation of JB6 P+ Mouse Epidermal Cells by Suppressing Cyclin-dependent Kinases and Phosphatidylinositol 3-Kinase

“…Phosphorylation of Rb by CDK4 contributes to the release and activation of E2F target genes, including those encoding E-and A-type cyclins, which facilitate progression through G 1 phase. In particular, Ser-795 and Ser-807/Ser-811 in Rb are specific sites for phosphorylation by CDK4 and are additionally phosphorylated by cyclin E-bound CDK2 (30,31). The G 1 /S-phase transition is tightly regulated by the interactions of the CDK4-cyclin D and CDK2-cyclin E complexes with Rb.…”