1GY3

pCDK2/cyclin A in complex with MgADP, nitrate and peptide substrate

Summary for 1GY3

• Entry DOI: 10.2210/pdb1gy3/pdb
• Related: 1AQ1 1B38 1B39 1BUH 1CKP 1DI8 1DM2 1E1V 1E1X 1E9H 1F5Q 1FIN 1FQ1 1FVT 1FVV 1G5S 1GIH 1GII 1GIJ 1HCK 1HCL 1JST 1JSU 1JSV 1JVP 1QMZ
• Descriptor: CELL DIVISION PROTEIN KINASE 2, CYCLIN A2, SUBSTRATE PEPTIDE, ... (8 entities in total)
• Functional Keywords: transferase-transferase substrate complex, cell cycle regulatory protein kinase, thr160-phospho-cyclin dependent protein kinase 2 in association with cyclin a, transferase- transferase substrate complex, transferase/transferase substrate
• Biological source: HOMO SAPIENS (HUMAN); More
• Total number of polymer chains: 6
• Total formula weight: 130578.76

Authors

Cook, A.,Lowe, E.D.,Chrysina, E.D.,Skamnaki, V.T.,Oikonomakos, N.G.,Johnson, L.N. (deposition date: 2002-04-19, release date: 2002-04-29, Last modification date: 2024-10-23)

Primary citation

Cook, A.,Lowe, E.D.,Chrysina, E.D.,Skamnaki, V.T.,Oikonomakos, N.G.,Johnson, L.N.
Structural Studies on Phospho-Cdk2/Cyclin a Bound to Nitrate, a Transition State Analogue: Implications for the Protein Kinase Mechanism
Biochemistry, 41:7301-, 2002

PubMed Abstract: Eukaryotic protein kinases catalyze the phosphoryl transfer of the gamma-phosphate of ATP to the serine, threonine, or tyrosine residue of protein substrates. The catalytic mechanism of phospho-CDK2/cyclin A (pCDK2/cyclin A) has been probed with structural and kinetic studies using the trigonal NO(3)(-) ion, which can be viewed as a mimic of the metaphosphate transition state. The crystal structure of pCDK2/cyclin A in complex with Mg(2+)ADP, nitrate, and a heptapeptide substrate has been determined at 2.7 A. The nitrate ion is located between the beta-phosphate of ADP and the hydroxyl group of the serine residue of the substrate. In one molecule of the asymmetric unit, the nitrate is close to the beta-phosphate of ADP (distance from the nitrate nitrogen to the nearest beta-phosphate oxygen of 2.5 A), while in the other subunit, the nitrate is closer to the substrate serine (distance of 2.1 A). Kinetic studies demonstrate that nitrate is not an effective inhibitor of protein kinases, consistent with the structural results that show the nitrate ion makes few stabilizing interactions with CDK2 at the catalytic site. The binding of orthovanadate was also investigated as a mimic of a pentavalent phosphorane intermediate of an associative mechanism for phosphoryl transfer. No vanadate was observed bound in a 3.4 A resolution structure of pCDK2/cyclin A in the presence of Mg(2+)ADP, and vanadate did not inhibit the kinase reaction. The results support the notion that the protein kinase reaction proceeds through a mostly dissociative mechanism with a trigonal planar metaphosphate intermediate rather than an associative mechanism that involves a pentavalent phosphorane intermediate.

PubMed: 12044161
DOI: 10.1021/BI0201724

Experimental method

X-RAY DIFFRACTION (2.7 Å)