PKA: a portrait of protein kinase dynamics

Protein kinases play a critical role in the integration of signaling networks in eukaryotic cells. cAMP-dependent protein kinase (PKA) serves as a prototype for this large and highly diverse enzyme family. The catalytic subunit of PKA provides the best example of how a protein kinase recognizes its substrates, as well as inhibitors, and also show how the enzyme moves through the steps of catalysis. Many of the relevant conformational states associated with the catalytic cycle which have been captured in a crystal lattice are summarized here. From these structures, we can begin to appreciate the molecular events of catalysis as well as the intricate orchestration of critical residues in the catalytic subunit that contribute to catalysis. The entire molecule participates. To fully understand signaling by PKA, however, requires an understanding of a large set of related proteins, not just the catalytic subunit. This includes the regulatory subunits that serve as receptors for cAMP and the A kinase anchoring proteins (AKAPs) that serve as scaffolds for PKA. The AKAPs localize PKA to specific sites in the cell by docking to the N-terminus of the regulatory subunits, thus creating microenvironments for PKA signaling. To fully appreciate the diversity and integration of these molecules, one needs not only high-resolution structures but also an appreciation of how these molecules behave in solution. Thus, in addition to obtaining high-resolution structures by X-ray crystallography and NMR, we have used fluorescent tools and also hydrogen/deuterium exchange coupled with mass spectrometry to probe the dynamic properties of these proteins and how they interact with one another. The molecular features of these molecules are described. Finally, we describe a new recombinantly expressed PKA reporter that allows us to monitor PKA activity in living cells.

The catalytic subunit of cAMP-dependent protein kinase: prototype for an extended network of communication

The protein kinase catalytic core in essence comprises an extended network of interactions that link distal parts of the molecule to the active site where they facilitate phosphoryl transfer from ATP to protein substrate. This review defines key sequence and structural elements, describes what is currently known about the molecular interactions, and how they are involved in catalysis.

Catalytic subunit of cyclic AMP-dependent protein kinase: structure and dynamics of the active site cleft

The catalytic subunit of cyclic AMP-dependent protein kinase serves as a structural template for the entire family of Ser, Thr, and Tyr specific protein kinases. We review here the dynamics of the active catalytic subunit. These dynamics correlate with an opening and closing of the active site cleft, and are considered to be a requirement for catalysis. The motions, described by a set of several crystal structures, reveal a very fluid active site cleft. This active site cleft with its dynamic opening and closing is a prime target for protein kinase inhibitors.

Protein kinase inhibition: natural and synthetic variations on a theme

How a protein kinase is turned off is as critical for its physiological function as is its catalytic activity. Examination of solved crystal structures representing different protein kinase subfamilies reveals a variety of strategies that are utilized by nature to lock protein kinases into inactive conformations. Pseudosubstrate and adenine mimetic mechanisms as well as complementarity to surfaces other than the active site are effective. Although most synthetic or natural product inhibitors target the active site, specifically the ATP binding site, a remarkably high degree of specificity can be achieved which is due to the extended surface of the protein that these inhibitors occupy. Although targeting of the ATP binding site is proving to be very successful, there is also wide latitude for designing inhibitors that target other surfaces of the kinases.

Bound to activate: conformational consequences of cyclin binding to CDK2

The cyclin-dependent kinases (CDKs) are among the most highly regulated enzymes in the protein-kinase family. The crystal structures of cyclin A and the CDK2-cyclin A complex spectacularly reveal the atomic basis for regulation of these enzymes and provide a template for understanding the function and regulation of other members of the CDK family.

How do protein kinases discriminate between serine/threonine and tyrosine? Structural insights from the insulin receptor protein-tyrosine kinase

The eukaryotic protein kinases that directly phosphorylate proteins are divided into two major classes: those that phosphorylate tyrosine and those that phosphorylate serine and threonine. Until recently, the similarities between these two classes of enzymes, which now total more than 400, were based primarily on sequence alignments. A recent report of the structure of the kinase domain (IRK) of the insulin receptor protein-tyrosine kinase now allows the features of these two families to be compared at the structural level. We review here this first tyrosine-specific protein kinase structure, and compare and contrast it to the structure of the serine/threonine-specific cAMP-dependent protein kinase. Although the general fold of the polypeptide backbone is conserved as predicted, unique features at the IRK active site provide a basis for understanding the differences in specificity for the phosphate acceptor amino acid. The structure of this inactive, dephosphorylated protein-tyrosine kinase also defines for the first time how activation might be achieved.

Domain movements in protein kinases

Structural studies of the catalytic subunit of the cAMP-dependent protein kinase, both by crystallographic methods and in solution, reveal two conformations. Crystal structures of several other protein kinases have also been solved in the past year. With this combined information we can begin to define mobile domains and subdomains within the conserved catalytic core.

Protein kinases share a common structural motif outside the conserved catalytic domain

A comparison of the sequences of the mammalian and Dictyostelium catalytic subunits of cAMP-dependent protein kinase revealed extensive sequence similarities through the catalytic core and the carboxy terminal tail. The amino terminal sequences however differ dramatically. The large difference in size, 73 kDa for the Dictyostelium enzyme versus 40 kDa is due to an extension in the N-terminus. The mouse enzyme has at its amino-terminus a long amphipatic helix, the A-helix, that precedes the catalytic core, covering the surface of both lobes of the enzyme. Dictyostelium does in fact, have a similar motif but it is remote from the catalytic core, in the N-terminal extension. On the basis of molecular modeling, it is proposed that residues 77-98 correspond to a structural motif similar to the A-helix in mouse catalytic subunit. Sequences encoding similar putative motifs contiguous to the catalytic core can be recognized in many other protein kinases and is particularly prominent in all of the non-receptor tyrosine kinases. In the case of Src, this A-helix motif appears to serve as the linker between the conserved catalytic core and the SH2 domain. The interaction between the A-helix motif and the core is described, and the general occurrence of this structure within the protein kinase family is discussed.

Three protein kinase structures define a common motif

Structural comparisons between cAMP-dependent protein kinase, cyclin-dependent kinase 2 and mitogen-activated protein kinase reveal which features are common to the protein kinase family and which are enzyme-specific.

A conserved helix motif complements the protein kinase core

Residues 40-300 of the mammalian catalytic (C) subunit of cAMP-dependent protein kinase define a conserved bilobal catalytic core shared by all eukaryotic protein kinases. Contiguous to the core is an extended amphipathic alpha-helix (A helix). Trp30, a prominent feature of this helix, fills a deep hydrophobic pocket between the two lobes on the surface opposite to the active site. The C subunit in Dictyostelium discoideum shows sequence conservation of residues 40-350 with the mouse enzyme but contains an N-terminal extension of 332 residues. A sequence corresponding to the A helix contiguous to the core is absent. However, we have now identified a remote A-helix motif (residues 77-98). When the core of the Dictyostelium C subunit was modeled, based on the mouse C subunit, complementarity between this putative A helix and the surface of the core was found to be conserved. Analysis of other protein kinases reveals that the A-helix motif is not restricted to cAMP-dependent protein kinase. In the Src-related family of protein kinases, for example, an A helix is very likely contiguous to the core, thus serving as a linker between the conserved catalytic core and the Src homology 2 domain. We predict that an A-helix motif complementary to the core will be a conserved feature of most eukaryotic protein kinases.

cAMP-dependent protein kinase defines a family of enzymes

The structure of the recombinant mouse catalytic subunit of cAMP-dependent protein kinase is reviewed with particular emphasis on the overall features and specific amino acids that are shared by all members of the eukaryotic protein kinase family. The crystal structure of a ternary complex containing both MgATP and a twenty-residue inhibitor peptide defines the precise role of the conserved residues that are clustered at the active site. In addition to catalysing the post-translational modification of other proteins, the catalytic subunit is itself subject to covalent modifications. It is a phosphoprotein and is also myristylated at its amino terminus. The enzyme when crystallized in the presence of detergent shows a detergent molecule bound to an acyl pocket that is presumably occupied by the myristyl moiety in the mammalian enzyme. When expressed in E. coli, the catalytic subunit is autophosphorylated at four sites. Two stable phosphates at Ser338 and Thr197 interact with multiple protein side chains thus explaining why they are inaccessible to phosphatases. Although all substrates and inhibitors of the catalytic subunit share a general minimum consensus sequence, the high affinity binding of protein inhibitors such as the regulatory subunits and the heat stable protein kinase inhibitors require additional determinants that lie beyond the consensus site. These two physiological inhibitors of the catalytic subunit appear to use different sites to achieve high-affinity binding.