Activation and Inhibition of Cyclin-dependent Kinase-2 by Phosphorylation; a Molecular Dynamics Study Reveals the Functional Importance of the Glycine-rich Loop

Overview

Journal Protein Sci

Specialty Biochemistry

Date 2004 May 11

PMID 15133164

Citations 31

Authors

Iveta Bartova

Michal Otyepka

Zdenek Kriz

Jaroslav Koca

Affiliations

Soon will be listed here.

Abstract

Nanoseconds long molecular dynamics (MD) trajectories of differently active complexes of human cyclin-dependent kinase 2 (inactive CDK2/ATP, semiactive CDK2/Cyclin A/ATP, fully active pT160-CDK2/Cyclin A/ATP, inhibited pT14-; pY15-; and pT14,pY15,pT160-CDK2/Cyclin A/ATP) were compared. The MD simulations results of CDK2 inhibition by phosphorylation at T14 and/or Y15 sites provide insight into the structural aspects of CDK2 deactivation. The inhibitory sites are localized in the glycine-rich loop (G-loop) positioned opposite the activation T-loop. Phosphorylation of T14 and both inhibitory sites T14 and Y15 together causes ATP misalignment for phosphorylation and G-loop conformational change. This conformational change leads to the opening of the CDK2 substrate binding box. The phosphorylated Y15 residue negatively affects substrate binding or its correct alignment for ATP terminal phospho-group transfer to the CDK2 substrate. The MD simulations of the CDK2 activation process provide results in agreement with previous X-ray data.

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References

Laaksonen L . A graphics program for the analysis and display of molecular dynamics trajectories. J Mol Graph. 1992; 10(1):33-4, 24. DOI: 10.1016/0263-7855(92)80007-z. View

Hanks S, Quinn A . Protein kinase catalytic domain sequence database: identification of conserved features of primary structure and classification of family members. Methods Enzymol. 1991; 200:38-62. DOI: 10.1016/0076-6879(91)00126-h. View

Sebastian B, Kakizuka A, Hunter T . Cdc25M2 activation of cyclin-dependent kinases by dephosphorylation of threonine-14 and tyrosine-15. Proc Natl Acad Sci U S A. 1993; 90(8):3521-4. PMC: 46332. DOI: 10.1073/pnas.90.8.3521. View

De Bondt H, Rosenblatt J, Jancarik J, Jones H, MORGAN D, Kim S . Crystal structure of cyclin-dependent kinase 2. Nature. 1993; 363(6430):595-602. DOI: 10.1038/363595a0. View

Watanabe N, Broome M, Hunter T . Regulation of the human WEE1Hu CDK tyrosine 15-kinase during the cell cycle. EMBO J. 1995; 14(9):1878-91. PMC: 398287. DOI: 10.1002/j.1460-2075.1995.tb07180.x. View

Jeffrey P, Russo A, Polyak K, Gibbs E, Hurwitz J, Massague J . Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex. Nature. 1995; 376(6538):313-20. DOI: 10.1038/376313a0. View

Poon R, Hunter T . Dephosphorylation of Cdk2 Thr160 by the cyclin-dependent kinase-interacting phosphatase KAP in the absence of cyclin. Science. 1995; 270(5233):90-3. DOI: 10.1126/science.270.5233.90. View

BRANDSEN J, Jones H, MORGAN D, Meijer L, Vesely J, Kim S . Multiple modes of ligand recognition: crystal structures of cyclin-dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine. Proteins. 1995; 22(4):378-91. DOI: 10.1002/prot.340220408. View

Philippopoulos M, Lim C . Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function. J Mol Biol. 1995; 254(4):771-92. DOI: 10.1006/jmbi.1995.0654. View

10.

Russo A, Jeffrey P, Pavletich N . Structural basis of cyclin-dependent kinase activation by phosphorylation. Nat Struct Biol. 1996; 3(8):696-700. DOI: 10.1038/nsb0896-696. View

11.

Holmes J, Solomon M . A predictive scale for evaluating cyclin-dependent kinase substrates. A comparison of p34cdc2 and p33cdk2. J Biol Chem. 1996; 271(41):25240-6. DOI: 10.1074/jbc.271.41.25240. View

12.

MORGAN D . The dynamics of cyclin dependent kinase structure. Curr Opin Cell Biol. 1996; 8(6):767-72. DOI: 10.1016/s0955-0674(96)80076-7. View

13.

Hemmer W, McGlone M, Tsigelny I, Taylor S . Role of the glycine triad in the ATP-binding site of cAMP-dependent protein kinase. J Biol Chem. 1997; 272(27):16946-54. DOI: 10.1074/jbc.272.27.16946. View

14.

MORGAN D . Cyclin-dependent kinases: engines, clocks, and microprocessors. Annu Rev Cell Dev Biol. 1997; 13:261-91. DOI: 10.1146/annurev.cellbio.13.1.261. View

15.

Jinno S, Hung S, Okayama H . Cell cycle start from quiescence controlled by tyrosine phosphorylation of Cdk4. Oncogene. 1999; 18(3):565-71. DOI: 10.1038/sj.onc.1202347. View

16.

Tsigelny I, Greenberg J, Cox S, Nichols W, Taylor S, Ten Eyck L . 600 ps molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase. Biopolymers. 1999; 50(5):513-24. DOI: 10.1002/(SICI)1097-0282(19991015)50:5<513::AID-BIP5>3.0.CO;2-I. View

17.

Holmes J, Solomon M . The role of Thr160 phosphorylation of Cdk2 in substrate recognition. Eur J Biochem. 2001; 268(17):4647-52. DOI: 10.1046/j.1432-1327.2001.02392.x. View

18.

Johnson L, Lewis R . Structural basis for control by phosphorylation. Chem Rev. 2001; 101(8):2209-42. DOI: 10.1021/cr000225s. View

19.

Johnson D, Akamine P, Radzio-Andzelm E, Madhusudan M, Taylor S . Dynamics of cAMP-dependent protein kinase. Chem Rev. 2001; 101(8):2243-70. DOI: 10.1021/cr000226k. View

20.

Cook A, Lowe E, Chrysina E, Skamnaki V, Oikonomakos N, Johnson L . Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism. Biochemistry. 2002; 41(23):7301-11. DOI: 10.1021/bi0201724. View