Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations
Language English Country Germany Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- Cyclin-Dependent Kinase 2 antagonists & inhibitors chemistry metabolism MeSH
- Phosphorylation MeSH
- Catalytic Domain MeSH
- Humans MeSH
- Protein Structure, Secondary MeSH
- Threonine chemistry metabolism MeSH
- Tyrosine chemistry metabolism MeSH
- Binding Sites MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Cyclin-Dependent Kinase 2 MeSH
- Threonine MeSH
- Tyrosine MeSH
The structures of fully active cyclin-dependent kinase-2 (CDK2) complexed with ATP and peptide substrate, CDK2 after the catalytic reaction, and CDK2 inhibited by phosphorylation at Thr14/Tyr15 were studied using molecular dynamics (MD) simulations. The structural details of the CDK2 catalytic site and CDK2 substrate binding box were described. Comparison of MD simulations of inhibited complexes of CDK2 was used to help understand the role of inhibitory phosphorylation at Thr14/Tyr15. Phosphorylation at Thr14/Tyr15 causes ATP misalignment for the phosphate-group transfer, changes in the Mg(2+) coordination sphere, and changes in the H-bond network formed by CDK2 catalytic residues (Asp127, Lys129, Asn132). The inhibitory phosphorylation causes the G-loop to shift from the ATP binding site, which leads to opening of the CDK2 substrate binding box, thus probably weakening substrate binding. All these effects explain the decrease in kinase activity observed after inhibitory phosphorylation at Thr14/Tyr15 in the G-loop. Interaction of the peptide substrate, and the phosphorylated peptide product, with CDK2 was also studied and compared. These results broaden hypotheses drawn from our previous MD studies as to why a basic residue (Arg/Lys) is preferred at the P(+2) substrate position.
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Nat Cell Biol. 1999 Nov;1(7):438-43 PubMed
Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3521-4 PubMed
Curr Biol. 1994 Nov 1;4(11):973-82 PubMed
Acc Chem Res. 2003 Jun;36(6):417-25 PubMed
Biochemistry. 1999 Nov 2;38(44):14718-30 PubMed
J Biol Chem. 2007 Feb 2;282(5):3173-81 PubMed
Protein Sci. 2008 Jan;17(1):22-33 PubMed
J Biol Chem. 2002 Jun 28;277(26):23847-53 PubMed
Chemistry. 2007;13(30):8437-44 PubMed
Science. 2002 Dec 6;298(5600):1912-34 PubMed
J Biol Chem. 1996 Oct 11;271(41):25240-6 PubMed
Biochemistry. 2002 Jun 11;41(23):7301-11 PubMed
Nature. 1995 Jul 27;376(6538):313-20 PubMed
J Am Chem Soc. 2005 Feb 9;127(5):1553-62 PubMed
Curr Opin Cell Biol. 2000 Dec;12(6):658-65 PubMed
J Biol Chem. 1999 Mar 26;274(13):8746-56 PubMed
Nature. 1989 Nov 2;342(6245):39-45 PubMed
EMBO J. 1992 Nov;11(11):3995-4005 PubMed
Nat Struct Biol. 1996 Aug;3(8):696-700 PubMed
Nature. 1995 Mar 9;374(6518):131-4 PubMed
Trends Pharmacol Sci. 2002 Sep;23(9):417-25 PubMed
Protein Sci. 2004 Jun;13(6):1449-57 PubMed
Protein Sci. 2005 Feb;14(2):445-51 PubMed
Cell. 1989 Jul 14;58(1):193-203 PubMed
Nature. 1993 Jun 17;363(6430):595-602 PubMed
Protein Sci. 2004 Aug;13(8):2059-77 PubMed
Annu Rev Cell Dev Biol. 1997;13:261-91 PubMed
J Biol Chem. 2006 Mar 17;281(11):7271-81 PubMed
Methods Enzymol. 1991;200:38-62 PubMed
EMBO J. 1995 May 1;14(9):1878-91 PubMed
