Cyclin Dependent protein kinases and the cell cycle (L13) Flashcards
How are CDKs activated?
By complex formation with cyclin
How are CDKs made catalytically competent?
By phosphorylation by CDK activating kinase
What are CDKs composed of?
Heterodimers of a catalytic CDK and a cyclin molecule
What are the 4 major stage stages of the cell cycle?
- The S phase- Entire DNA duplicated and chromoomes doubled
- Gap G2
- M phase- mitosis
- Gap G1
Why are there halts in the cell cycle?
May allow damaged DNA to be corrected or may prevent its replication, or may initiate apoptosis is the cell is beyond repair
How are CDKs and the cell cycle related?
The activated CDKs are effectively a series of switches which govern the passage of the cell through the steps
Statutory CDK mediated halts and intervals in the cell cycle, and brakes on proliferation, only occurs if the relevant CDKs are inhibited
Successful phosphorylation of their target proteins by the CDKs gives reaction products which themselves are crucial to the controlled progression of the cell cycle
What is the primary target of the G1 CDK4/6-cycline D complex?
pRb
How are CDKs involved in cell cycle control?
Phosphorylation of pRB activates the E2F transcription factor family to transcribe the G1 to S checkpoint cyclin E and the S phase cyclin A.
The active CDK2-cyclin E complex sustains pRB phosphorylation (inactivation) and thus supports entry into the S phase and replication (inhib prolongs the G1 phase)
How does p53 and p21 limit the proliferation controlled by the G1 to S ans S phase complexes?
p21 and p27 are members of the cip/kip family of CKIs.
The INK family of inhibitors includes p16
p53 downregulates pRB, perhaps to sustain E2F activity following degradation of the G1 and G1/S CDK- cyclin complexes which inactivate pRb.
p53 also promotes apoptosis
What is p53 activated by?
MAP kinase
What effect will mutation or loss of Rb tumor suppressor gene have?
Uncontrolled transcription by E2F
What effect will mutation or loss of CDK2-cyclin E inhibition have?
Free pass through the G1-S checkpoint
What effect will mutation or loss of CDK2-cyclin A inhibition have?
Remove controlling restraints within the S phase
What is the structure of Cyclin A?
Two similar domains, each with 5 alpha helices. The domain is called the cyclin fold.
The N-terminal domain has an amino acid sequence that is strongly conserved in all cyclins= cyclin box
What is the structure of CDK2?
Folded into 2 domains
The N-terminal domain comprises a 5 starnded beta-sheet and an alpha-helix that has the PSTAIRE sequence
The PSTAIRE helix (C helix) highly conserved in all protein kinases with the E being Glu51.
C-term domain is mainly alpha helical and contains a flexible loop region called the T-loop or activation loop which includes Thr160 which is phosphorylated in the fully active enzyme
How does CDK2 interact with cyclin A?
The cyclin box interacts with the PSTAIRE helix and the T-loop of CDK2
CDK2 undergoes major conformational changes
Describe the ATP binding site in the active CDK-cyclin complex
Mg ion present
In the active complex, Lys33 forms a salt bridge to Glu51 at the end of the PSTAIRE helix and Asp145
The adenosine moiety is H bonded to the hinge region
Detail the structural changes in active CDK which confers activity
- The T-loop is completely rearranged, with movements of up to 20 Amstrongs and with the alpha helix being replaced by a beta-strand. The active site become exposed to allow entry to protein substratesand conformations of essential residues are altered incl Asp145 which ligates to the Mg atom in the active site
- The PSTAIRE helix moves closer to the active site cleft and rotates by ~90 degrees so that the catalytically essential residue Glu51 points into the cleft rather than away from it and forms salt bridge with the ATP phosphate binding Lys33 in preceding strand.
- Gly flap moves away from the ATP site to allow entry to protein substrates and access to the ATP
- The whole of the N-terminal domain rotates slightly with respect to the C-term domain
What structural changes of CDK2 occur on cyclin binding?
The T-loop changes its structure, pThr60 interacts with Arg50, and the active site becomes open and pThr160 positioned to interact with the portein substrate
How are protein substrates recognised by CDK2-cyclin A?
Bind in the deep cleft between the 2 domains
Recognised through sequence S/T-P-X-K/R
Extensive interactions between the bound peptide and the main chain atoms of residues 162-165 in the T-loop
The substrate protein in recruited by the complex through recognition by the cyclin
How is CDK2-cyclin A inhibited?
Natural inhibitory phosphorylation by CDK kinases at sites other than Thr160
Natural inhibition by CDK inhibitors which bind to both CDK2 and cyclin A and block the ATP site
Designed active CDK2 inhibitors which occupy the ATP site
How does a CDK kinase inhibit CDK2-cyclin A?
Phosphorylation blocks protein substrate binding, preventing access to the ATP site and disrupts interactions of key residues with the ATP phosphates
There are 2 inhibitory sites present on the Gly flap at Thr14 and Tyr15
How does a drug inhibit CDK2-cyclin A?
The structure of both the hinge and the Gly flap change in response to drug.
All other regions crucial to activity remain unchanged and peptide binding may still be possible with small movement of the Gly flap
