To better understand the mechanism of ligand binding and ligand-induced conformational change, the crystal structure of apoenzyme catalytic (C) subunit of adenosine-3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) was solved. The apoenzyme structure (Apo) provides a snapshot of the enzyme in the first step of the catalytic cycle, and in this unliganded form the PKA C subunit adopts an open conformation ...
To better understand the mechanism of ligand binding and ligand-induced conformational change, the crystal structure of apoenzyme catalytic (C) subunit of adenosine-3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) was solved. The apoenzyme structure (Apo) provides a snapshot of the enzyme in the first step of the catalytic cycle, and in this unliganded form the PKA C subunit adopts an open conformation. A hydrophobic junction is formed by residues from the small and large lobes that come into close contact. This "greasy" patch may lubricate the shearing motion associated with domain rotation, and the opening and closing of the active-site cleft. Although Apo appears to be quite dynamic, many important residues for MgATP binding and phosphoryl transfer in the active site are preformed. Residues around the adenine ring of ATP and residues involved in phosphoryl transfer from the large lobe are mostly preformed, whereas residues involved in ribose binding and in the Gly-rich loop are not. Prior to ligand binding, Lys72 and the C-terminal tail, two important ATP-binding elements are also disordered. The surface created in the active site is contoured to bind ATP, but not GTP, and appears to be held in place by a stable hydrophobic core, which includes helices C, E, and F, and beta strand 6. This core seems to provide a network for communicating from the active site, where nucleotide binds, to the peripheral peptide-binding F-to-G helix loop, exemplified by Phe239. Two potential lines of communication are the D helix and the F helix. The conserved Trp222-Phe238 network, which lies adjacent to the F-to-G helix loop, suggests that this network would exist in other protein kinases and may be a conserved means of communicating ATP binding from the active site to the distal peptide-binding ledge.
Related Citations:
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase Madhusudan, Akamine, P., Xuong, N.H., Taylor, S.S. (2002) Nat Struct Biol 9: 273
Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation Karlsson, R., Zheng, J., Xuong, N., Taylor, S.S., Sowadski, J.M. (1993) Acta Crystallogr D Biol Crystallogr 49: 381
Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations Zheng, J., Knighton, D.R., Xuong, N.H., Taylor, S.S., Sowadski, J.M., Ten Eyck, L.F. (1993) Protein Sci 2: 1559
Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor Zheng, J., Knighton, D.R., Ten Eyck, L.F., Karlsson, R., Xuong, N., Taylor, S.S., Sowadski, J.M. (1993) Biochemistry 32: 2154
A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility Narayana, N., Cox, S., Nguyen-huu, X., Ten Eyck, L.F., Taylor, S.S. (1997) Structure 5: 921
Organizational Affiliation:
Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA.
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