Regulatory Subunit Dimer Research Articles

A mutation in the PRKAR1B gene drives pathological mechanisms of neurodegeneration across species.

Protein Kinase A (PKA) neuronal function is controlled by the interaction of a regulatory (R) subunit dimer to two catalytic (C) subunits. Recently, the L50R variant in the gene encoding the RIβ subunit was identified in individuals with a novel neurodegenerative disease. However, the mechanisms driving the disease phenotype remained unknown. In this study, we generated a mouse model carrying the RIβ-L50R mutation to replicate the human disease phenotype and study its progression with age. We examined postmortem brains of affected individuals as well as live cell cultures. Employing biochemical assays, immunohistochemistry, and behavioral assessments, we investigated the impact of the mutation on PKA complex assembly, protein aggregation and neuronal degeneration. We reveal that RIβ is an aggregation-prone protein that progressively accumulates in wildtype and Alzheimer's mouse models with age, while aggregation is accelerated in the RIβ-L50R mouse model. We define RIβ-L50R as a causal mutation driving an age-dependent behavioral and disease phenotype in human and mouse models. Mechanistically, this mutation disrupts RIβ dimerization, leading to aggregation of its monomers. Intriguingly, interaction with the C-subunit protects the RIβ-L50R from self-aggregating, in a dose-dependent manner. Furthermore, cAMP signaling induces RIβ-L50R aggregation. The pathophysiological mechanism elucidated here for a newly recognized neurodegenerative disease, in which protein aggregation is the result of disrupted homodimerization, sheds light on a remarkably under-appreciated but potentially common mechanism across several neurodegenerative diseases.

Assembly of nuclear dimers of PI3K regulatory subunits is regulated by the Cdc42-activated tyrosine kinase ACK

Activated Cdc42-associated kinase (ACK) is an oncogenic nonreceptor tyrosine kinase associated with poor prognosis in several human cancers. ACK promotes proliferation, in part by contributing to the activation of Akt, the major effector of class 1A phosphoinositide 3-kinases (PI3Ks), which transduce signals via membrane phosphoinositol lipids. We now show that ACK also interacts with other key components of class 1A PI3K signaling, the PI3K regulatory subunits. We demonstrate ACK binds to all five PI3K regulatory subunit isoforms and directly phosphorylates p85α, p85β, p50α, and p55α on Tyr607 (or analogous residues). We found that phosphorylation of p85β promotes cell proliferation in HEK293T cells. We demonstrate that ACK interacts with p85α exclusively in nuclear-enriched cell fractions, where p85α phosphorylated at Tyr607 (pTyr607) also resides, and identify an interaction between pTyr607 and the N-terminal SH2 domain that supports dimerization of the regulatory subunits. We infer from this that ACK targets p110-independent p85 and further postulate that these regulatory subunit dimers undertake novel nuclear functions underpinning ACK activity. We conclude that these dimers represent a previously undescribed mode of regulation for the class1A PI3K regulatory subunits and potentially reveal additional avenues for therapeutic intervention.

Heat stress regulates the expression of TPK1 gene at transcriptional and post-transcriptional levels in Saccharomyces cerevisiae.

In Saccharomyces cerevisiae cAMP regulates different cellular processes through PKA. The specificity of the response of the cAMP-PKA pathway is highly regulated. Here we address the mechanism through which the cAMP-PKA pathway mediates its response to heat shock and thermal adaptation in yeast. PKA holoenzyme is composed of a regulatory subunit dimer (Bcy1) and two catalytic subunits (Tpk1, Tpk2, or Tpk3). PKA subunits are differentially expressed under certain growth conditions. Here we demonstrate the increased abundance and half-life of TPK1 mRNA and the assembly of this mRNA in cytoplasmic foci during heat shock at 37°C. The resistance of the foci to cycloheximide-induced disassembly along with the polysome profiling analysis suggest that TPK1 mRNA is impaired for entry into translation. TPK1 expression was also evaluated during a recurrent heat shock and thermal adaptation. Tpk1 protein level is significantly increased during the recovery periods. The crosstalk of cAMP-PKA pathway and CWI signalling was also studied. Wsc3 sensor and some components of the CWI pathway are necessary for the TPK1 expression upon heat shock. The assembly in foci upon thermal stress depends on Wsc3. Tpk1 expression is lower in a wsc3∆ mutant than in WT strain during thermal adaptation and thus the PKA levels are also lower. An increase in Tpk1 abundance in the PKA holoenzyme in response to heat shock is presented, suggesting that a recurrent stress enhanced the fitness for the coming favourable conditions. Therefore, the regulation of TPK1 expression by thermal stress contributes to the specificity of cAMP-PKA signalling.

Spatial Organization of a cAMP/Ca2+‐Regulated Signaling Complex: A Structural Study of an AKAP79‐Scaffolded Complex Containing Type IIβ PKA and Calcineurin

cAMP‐dependent protein kinase (PKA) regulates many cell processes including development, differentiation, and memory. In its resting state, PKA is a tetrameric holoenzyme consisting of a regulatory (R) subunit dimer and two catalytic (C) subunits. Four isoforms of the R‐subunit exist (RIα, RIβ, RIIα, and RIIβ). Although each isoform varies in sequence and quaternary structure, all share a common domain organization. The strength, duration, and specificity of PKA activity within the cell are mostly dependent upon isoform‐specific subcellular localization. The D/D domain interface of the R‐ subunits serves as a docking site for A Kinase Anchoring Proteins (AKAPs) that target PKA to specific cellular locations. In cardiac myocytes and neurons, PKA is localized to Cav1.2 L‐type calcium channels by AKAP79 and up‐regulates calcium influx by phosphorylating the channel's cytosolic C‐terminal tail. AKAP79 also binds the Ca2+/calmodulin‐dependent protein phosphatase type 2B (PP2B, or calcineurin) at a site very close to that of PKA binding. Given the close proximity of the calcineurin and PKA binding sites on AKAP79, calcineurin has been suggested to play roles in the regulation of calcium channels, along with regulation of PKA activity itself. Using a variety of biochemical and biophysical techniques, we have isolated and characterized a stable complex of the C‐terminal tail of AKAP79, RIIβ holoenzyme, and calciuneurin (“ARC” for short). We show a stoichiometry of 1:1:1 (AKAP79ct: RIIβ2‐C2 :CNt) using native mass spectroscopy, and SAXS/SANS techniques confirm that this is a compact complex, suggesting a close interaction between PKA and calcineurin when bound to AKAP79. Altogether, we suggest beyond its function of localizing PKA and CN in close spatial proximity to the Cav1.2 L‐type calcium channel, the ARC signalosome fosters extended protein‐protein interactions and regulations that suggest tight spatiotemporal control. Support for this work was provided through NIH GM034921.Support or Funding InformationJames Hall is an IRACDA fellow and was supported by NIGMS/NIH award K12GM068524. This work was also supported by a grant from the National Institutes of Health GM034921 to S.S. Taylor. This Research used resources at the High Flux Isotope Reactor and Spallation Neutron Source, which are DOE Office of Science User Facilities operated by Oak Ridge National Laboratory. This work utilized SasView software, originally developed by the DANSE project under NSF award DMR‐0520547.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

The Molecular Basis for Specificity at the Level of the Protein Kinase a Catalytic Subunit

Assembly of multi enzyme complexes at subcellular localizations by anchoring- and scaffolding proteins represents a pivotal mechanism for achieving spatiotemporal regulation of cellular signaling after hormone receptor targeting [for review, see (1)]. In the 3′ 5′-cyclic adenosine monophosphate (cAMP) dependent protein kinase (PKA) signaling pathway it is generally accepted that specificity is secured at several levels. This includes at the first level stimulation of receptors coupled to heterotrimeric G proteins which through stimulation of adenylyl cyclase (AC) forms the second messenger cAMP. Cyclic AMP has several receptors including PKA. PKA is a tetrameric holoenzyme consisting of a regulatory (R) subunit dimer and two catalytic (C) subunits. The R subunit is the receptor for cAMP and compartmentalizes cAMP signals through binding to cell and tissue-specifically expressed A kinase anchoring proteins (AKAPs). The current dogma tells that in the presence of cAMP, PKA dissociates into an R subunit dimer and two C subunits which are free to phosphorylate relevant substrates in the cytosol and nucleus. The release of the C subunit has raised the question how specificity of the cAMP and PKA signaling pathway is maintained when the C subunit no longer is attached to the R subunit-AKAP complex. An increasing body of evidence points toward a regulatory role of the cAMP and PKA signaling pathway by targeting the C subunits to various C subunit binding proteins in the cytosol and nucleus. Moreover, recent identification of isoform specific amino acid sequences, motifs and three dimensional structures have together provided new insight into how PKA at the level of the C subunit may act in a highly isoform-specific fashion. Here we discuss recent understanding of specificity of the cAMP and PKA signaling pathway based on C subunit subcellular targeting as well as evolution of the C subunit structure that may contribute to the dynamic regulation of C subunit activity.

Spatial Organization of a cAMP/Ca2+‐Regulated Signaling Complex: A Solution Structural Small‐Angle X‐ray and Neutron Scattering Study of an AKAP79‐Scaffolded Complex Containing Type IIβ PKA and Calcineurin

cAMP‐dependent protein kinase (PKA) regulates many cell processes including development, differentiation, and memory. In its resting state, PKA is a tetrameric holoenzyme consisting of a regulatory (R) subunit dimer and two catalytic (C) subunits. Four isoforms of the R‐subunit exist (RIα, RIβ, RIIα, and RIIβ). Although each isoform varies in sequence and quaternary structure, all share a common domain organization. The strength, duration, and specificity of PKA activity within the cell are mostly dependent upon isoform specific subcellular localization. The D/D domain interface of the R‐subunits serves as a docking site for A Kinase Anchoring Proteins (AKAPs) that target PKA to specific cellular locations. In cardiac myocytes and neurons, PKA is localized to Cav1.2 L‐type calcium channels by AKAP79 and up‐regulates calcium influx by phosphorylating the channel's cytosolic C‐terminal tail. AKAP79 also binds the Ca2+/calmodulin‐dependent protein phosphatase type 2B (PP2B, or calcineurin) at a site very close to that of PKA binding. Given the close proximity of the calcineurin and PKA binding sites on AKAP79, calcineurin has been suggested to play roles in regulation of calcium channels, along with regulation of PKA activity itself. Using a variety of biochemical and biophysical techniques, we have isolated and characterized a stable complex of the C‐terminal tail of AKAP79, RIIβ holoenzyme, and calcuneurin (“ARC” for short). We show a stoichiometry of 1:1:1 (AKAP79: RIIβ2C2:CN) using native mass spectroscopy, and SAXS/SANS techniques confirm that this is a compact complex, suggesting a close interaction between PKA and calcineurin when bound to AKAP79. Altogether, we suggest beyond its function of localizing PKA and CN in close spatial proximity to the Cav1.2 L‐type calcium channel, the ARC signalosome fosters extended protein‐protein interactions and regulations that suggest tight spatiotemporal control.Support or Funding InformationJames Hall is a San Diego IRACDA Fellow supported by National Institutes of Health (NIH)/NIGMS K12 GM06852 Award. Support for this work was provided through NIH GM034921.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

174 - Modulation of Cardiac Function by Oxidized Type I Protein Kinase A

L-type Ca2+ channels (LTCC) are known to be involved in the dysregulation of intracellular Ca2+ handling in heart failure (HF) contributing to contractile dysfunction and arrhythmias. Beside alteration in subcellular localization, reduced LTCC function may be a consequence of altered posttranslational modification. It is known that cAMP-dependent protein kinase A (PKA) can phosphorylate LTCC resulting in increased Ca2+ current (ICa). PKA-dependent LTCC phosphorylation has been shown to occur upon acute pressure overload partly compensating for reduced Ca2+ release from sarcoplasmic reticulum (SR). However, the mechanisms of PKA-dependent LTCC activation upon pressure overload are inadequately understood. Recent data suggest that PKA can be activated upon direct oxidation of its regulatory subunit (RI) without binding to its physiologic agonist, cAMP. In this thesis, I have investigated the pathophysiological relevance of this oxidative PKA activation for intracellular Ca2+ homeostasis, contractile function, and arrhythmogenesis upon pressure overload. Here, a novel PKA redox-dead knock-in mouse line was used harboring a RI point mutation that results in the exchange of cysteine 17 with serine (KI). Oxidation of cysteine 17 with consequent intersubunit disulfide bridge, RI-RI dimer, formation is inhibited. The later is a prerequisite for catalytic subunit release and phosphorylation of target proteins, i.e. oxidative activation of the kinase. At baseline, no alterations in Ca2+ handling (FURA-2-loaded isolated cardiomyocytes) or contractile function (echocardiography) are observed in these mice. However, NAPDH oxidase 2 (NOX2)-dependent oxidants stimulated by angiotensin II (AngII, 1µmol/L) could not result in RI dimer (Western blotting) formation in KI. In accordance, ICa and Ca2+ transient amplitude were significantly smaller in KI mice in the presence of AngII. Similarly, pressure overload by transverse aortic constriction did not result in RI dimer formation in KI. Moreover, compared to WT mice KI mice displayed significantly reduced ICa and Ca2+ transient amplitude with a significantly impaired ejection fraction (echocardiography) upon pressure overload. Western blot analyses revealed that AngII and pressure overload-dependent LTCC phosphorylation at the PKA site were inhibited. Beside disturbed contractile function, KI mice displayed severe QTc prolongation and increased the propensity for ventricular arrhythmias (ECG and programmed ventricular stimulation), which results in significantly reduced survival rates upon pressure overload. In summary, oxidative activation of PKA appears to be important for adaptation of the heart during increased afterload. Thus, stimulation of oxidative PKA activation could be a potential therapeutic option for patients with cardiac diseases, like heart failure.

Ablation of the Cβ2 subunit of PKA in immune cells leads to increased susceptibility to systemic inflammation in mice.

Protein kinase A (PKA) is a holoenzyme composed of a regulatory subunit dimer and two catalytic subunits and regulates numerous cellular functions including immune cell activity. There are two major catalytic subunit genes, PRKACA and PRKACB encoding the catalytic subunits Cα and Cβ. The PRKACB gene encodes several splice variants including Cβ2, which is enriched in T-, B- and natural killer cells. Cβ2 is significantly larger (46kDa) than any other C splice variant. In this study we characterized mice ablated for the Cβ2 protein demonstrating a significantly reduced cAMP-induced catalytic activity of PKA in the spleenocytes, lymphocytes and thymocytes. We also observed a significantly increased number of CD62L-expressing CD4+ and CD8+ T cells in LNs, accompanied by increased susceptibility to systemic inflammation by the Cβ2 ablated mice. The latter was reflected in an elevated sensitivity to collagen-induced arthritis (CIA), as well as higher concentration of TNF-α and lower concentration of IL-10 in response to LPS challenges. We suggest a role of Cβ2 in regulating innate as well as adaptive immune sensitivity invivo.

PKA: Dynamic Assembly and Regulation of Macromolecular Signaling Complexes

PKA Signaling: Linkers, Loops, and Intrinsically Disorder Regions Drive the Dynamic Assembly of Holoenzyme Complexes.The PKA catalytic (C) subunit crystallized in 1991, gave us our first glimpse of the fold that describes all protein kinases. The two lobes that comprise the core are flanked by N-and C-terminal tails, which wrap around both lobes. By capturing all stages of catalysis in crystal structures we appreciate the dynamic nature of these tails and how they undergo order-disorder transitions as part of the catalytic cycle. Ordering the activation loop by a critical phosphate is another fundamental order/disorder transition that is a conserved feature of most protein kinases. These dynamic features allow the kinases to function as highly regulated molecular switches. In the case of PKA, the C-subunit is packaged with regulatory (R) subunit dimers where each chain contains two C-terminal cAMP binding (CNB) domains. The CNB domains are highly dynamic allosteric signaling modules that have been conserved to translate a biological response to cAMP. Although the fundamental features of this domain were elucidated by structures of R-monomers and R:C heterodimers, it required full-length R2C2 tetramers to appreciate the importance of symmetry for PKA signaling. Each R-subunit contains an N-terminal dimerization domain that is also a docking site for scaffold proteins referred to as A Kinase Anchoring Proteins (AKAPs). This domain is joined by a flexible linker to the CNB domains, and embedded within the linker is an inhibitor site that docks to the active site of the C-subunit in the holoenzyme. The order/disorder transitions of the linker drive the assembly of the holoenzymes which each have distinct quaternary structures. The linkers, rich in biological information, are an essential feature of PKA regulation. (Funded by NIH GM34921 and DK54441.)

Hematopoietic neoplasms in Prkar2a-deficient mice.

BackgroundProtein kinase A (PKA) is a holoenzyme that consists of a dimer of regulatory subunits and two inactive catalytic subunits that bind to the regulatory subunit dimer. Four regulatory subunits (RIα, RIβ, RIIα, RIIβ) and four catalytic subunits (Cα, Cβ, Cγ, Prkx) have been described in the human and mouse genomes. Previous studies showed that complete inactivation of the Prkar1a subunit (coding for RIα) in the germline leads to embryonic lethality, while Prkar1a–deficient mice are viable and develop schwannomas, thyroid, and bone neoplasms, and rarely lymphomas and sarcomas. Mice with inactivation of the Prkar2a and Prkar2b genes (coding for RIIα and RIIβ, respectively) are also viable but have not been studied for their susceptibility to any tumors.MethodsCohorts of Prkar1a+/−, Prkar2a+/−, Prkar2a−/−, Prkar2b+/− and wild type (WT) mice have been observed between 5 and 25 months of age for the development of hematologic malignancies. Tissues were studied by immunohistochemistry; tumor-specific markers were also used as indicated. Cell sorting and protein studies were also performed.ResultsBoth Prkar2a−/− and Prkar2a+/− mice frequently developed hematopoietic neoplasms dominated by histiocytic sarcomas (HS) with rare diffuse large B cell lymphomas (DLBCL). Southern blot analysis confirmed that the tumors diagnosed histologically as DLBCL were clonal B cell neoplasms. Mice with other genotypes did not develop a significant number of similar neoplasms.ConclusionsPrkar2a deficiency predisposes to hematopoietic malignancies in vivo. RIIα’s likely association with HS and DLBCL was hitherto unrecognized and may lead to better understanding of these rare neoplasms.

Using Markov State Models to Develop a Mechanistic Understanding of Protein Kinase A Regulatory Subunit RIα Activation in Response to cAMP Binding

Protein kinase A (PKA) holoenzyme consists of two catalytic (C) subunits and a regulatory (R) subunit dimer (R(2)C(2)). The kinase is activated by the binding of cAMPs to the two cyclic nucleotide binding domains (CBDs), A and B, on each R-subunit. Despite extensive study, details of the allosteric mechanisms underlying the cooperativity of holoenzyme activation remain unclear. Several Markov state models of PKA-RIα were developed to test competing theories of activation for the R(2)C(2) complex. We found that CBD-B plays an essential role in R-C interaction and promotes the release of the first C-subunit prior to the binding to CBD-A. This favors a conformational selection mechanism for release of the first C-subunit of PKA. However, the release of the second C-subunit requires all four cAMP sites to be occupied. These analyses elucidate R-C heterodimer interactions in the cooperative activation of PKA and cAMP binding and represent a new mechanistic model of R(2)C(2) PKA-RIα activation.

Quaternary architecture of PKA RIβ holoenzyme reveals isoform diversity (802.5)

The cAMP‐dependent protein kinase A (PKA) holoenzyme is composed of two catalytic (C) subunits and a regulatory (R) subunit dimer. Although much is known about the structures and function of RIα, RIIα and RIIβ isoforms, little is known about RIβ. Given its unique biological importance and functional non‐redundancy, we hypothesized that RIβ will also have unique structural properties. We show first that the RIβ2:C2 overall quaternary structure is different from RIα2:C2, its closest homolog, using small angle x‐ray scattering (SAXS). We found that RIβ is more enriched in mouse mitochondria than RIα. We then obtained a crystal structure of the tetramer holoenzyme with the full‐length RIβ bound to the C‐subunit. This is the first PKA tetramer structure where all the domains can be visualized. The head‐to‐head alignment of the C‐subunits is in striking contrast to RIα where the C‐subunits do not contact each other. The structure allows us to appreciate how assembly of the R2:C2 complex creates isoform diversity even though the conformations of the R:C heterodimers are similar in all isoforms. Conserved tertiary structure does not translate into conserved quaternary structure. This structure paves the way for exploring the biological properties of RIβ.

Assembly of Protein Kinase a RIIβ Macromolecular Complexes

Protein Kinase A is assembled in cells as an inactive tetrameric holoenzyme with Regulatory-subunit dimers and two Catalytic-subunits. In mammalian cells there are four functionally non-redundant R-subunits (RIα, RIβ, RIIα and RIIβ). Although all R-subunits share the same domain organization, the quaternary structures of each holoenzyme are unique and their allosteric mechanisms for activation differ from one another. In order to understand PKA signaling in cells, we now need to go beyond PKA holoenyzme and look at how PKA is scaffolded with other signaling proteins into macromolecular complexes that are targeted by A Kinase Anchoring Proteins (AKAPs) to channels, receptors, and transporters in cells. Most AKAPs are RII specific. AKAPs can not only recruit PKA to specific cellular sites but can also bring PKA to the vicinity of its substrates and other signaling proteins such as adenylate cyclases, phosphodiesterases, and phosphatases. This creates a mechanism to control the cellular actionsof PKA both spatially and temporally. The PKA-AKAP79-calcineurin (CaN) complex presents a highly approachable system for examining PKA macromolecular signaling scaffolds. It serves at least two purposes: positioning CaN and PKA near critical substrates, and focusing Ca2+ and cAMP signaling in “microdomains” built around voltage gated Ca2+ channels. PKA phosphorylates and activates the Ca2+ channel. Ca2+ then enters the cell and binds to CaN and anchored calmodulin. Activated CaN can then dephosphorylate the channel, decreasing its activity. Furthermore CaN dephosphorylates the RIIβ regulatory subunit of PKA, promoting its binding to the catalytic subunit and inactivation of PKA. We used small angle solution scattering and native mass spectrometry methods to study the stoichiometry and structure of this macromolecular complex. We also found that Ca2+ can support the single turnover of phosphate in the RIIβ holoenzyme although it cannot support steady state catalysis.

Molecular Dynamics Simulations of the Catalytic Subunit of Protein Kinase a Reveal New Insight into the Catalytic Process

Protein kinases chemically add phosphate groups to target proteins. Phosphorylation usually results in a functional change of the target protein, and serves as a regulatory mechanism to elicit a response to a stimulus at the cellular or organism level. Protein kinase A (PKA) was first characterized in 1968 and is considered to be the prototype for the entire kinome. The inactive form of PKA is a heterotetramer of two catalytic subunits (PKAc) that are bound to each member of a regulatory subunit (PKAr) dimer. PKA activates when two cyclic-AMPs bind to each of the PKAr, which releases the PKAc to perform the phosphorylation reaction on a polypeptide substrate. PKAc has two lobes that flank the active site: a small N-terminal lobe that is primarily associated with binding and positioning ATP, and a large lobe that provides a docking surface for substrates or inhibitor proteins. PKAc has three major conformational states: open, intermediate and closed. Despite its early discovery, its activation and deactivation is still not fully understood. Although NMR spin relaxation experiments have probed local dynamics, the movements of the PKAc domains, that may be related to its biological activity, have not been directly examined. To gain new insight into the role that PKAc dynamics plays in the phosphotransfer reaction, we performed microsecond long molecular dynamics simulations of apo-PKAc, PKAc-ATP (intermediate) and PKAc-ATP-substrate peptide (closed, reactive) and PKAc-ATP-inhibitor peptide (closed, nonreactive) complexes. By applying a network-based analysis method, we found conformational communities for PKAc in the various states that made it possible to identify critical residues and structural transitions involved in the catalytic process.

Localization and quaternary structure of the PKA RIβ holoenzyme

Specificity for signaling by cAMP-dependent protein kinase (PKA) is achieved by both targeting and isoform diversity. The inactive PKA holoenzyme has two catalytic (C) subunits and a regulatory (R) subunit dimer (R(2):C(2)). Although the RIα, RIIα, and RIIβ isoforms are well studied, little is known about RIβ. We show here that RIβ is enriched selectively in mitochondria and hypothesized that its unique biological importance and functional nonredundancy will correlate with its structure. Small-angle X-ray scattering showed that the overall shape of RIβ(2):C(2) is different from its closest homolog, RIα(2):C(2). The full-length RIβ(2):C(2) crystal structure allows us to visualize all the domains of the PKA holoenzyme complex and shows how isoform-specific assembly of holoenzyme complexes can create distinct quaternary structures even though the R(1):C(1) heterodimers are similar in all isoforms. The creation of discrete isoform-specific PKA holoenzyme signaling "foci" paves the way for exploring further biological roles of PKA RIβ and establishes a paradigm for PKA signaling.

Structure and allostery of the PKA RIIβ tetrameric holoenzyme.

In its physiological state, cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is a tetramer that contains a regulatory (R) subunit dimer and two catalytic (C) subunits. We describe here the 2.3 angstrom structure of full-length tetrameric RIIβ(2):C(2) holoenzyme. This structure showing a dimer of dimers provides a mechanistic understanding of allosteric activation by cAMP. The heterodimers are anchored together by an interface created by the β4-β5 loop in the RIIβ subunit, which docks onto the carboxyl-terminal tail of the adjacent C subunit, thereby forcing the C subunit into a fully closed conformation in the absence of nucleotide. Diffusion of magnesium adenosine triphosphate (ATP) into these crystals trapped not ATP, but the reaction products, adenosine diphosphate and the phosphorylated RIIβ subunit. This complex has implications for the dissociation-reassociation cycling of PKA. The quaternary structure of the RIIβ tetramer differs appreciably from our model of the RIα tetramer, confirming the small-angle x-ray scattering prediction that the structures of each PKA tetramer are different.

Critical and synergy nodes in insulin-EGF signaling network

Protein kinases play a predominant regulatory role in nearly every aspect of cell biology and they can modify the function of a protein in almost every conceivable way. Protein phosphorylation can increase or decrease enzyme activity and it can alter other biological activities such as transcription and translation. Moreover, some phosphorylation sites on a given protein are stimulatory while others are inhibitory. The human protein kinase gene family consists of 518 members along with 106 pseudogenes. Furthermore, about 50 of the 518 gene products lack important catalytic residues and are called protein pseudokinases. The non-catalytic allosteric interaction of protein kinases and pseudokinases with other proteins has added an important regulatory feature to the biochemistry and cell biology of the protein kinase superfamily. With rare exceptions, a divalent cation such as Mg2+ is required for the reaction. All protein kinases exist in a basal state and are activated only as necessary by divergent regulatory stimuli. The mechanisms for switching between dormant and active protein kinases can be intricate. Phosphorylase kinase was the first protein kinase to be characterized biochemically and the mechanism of its regulation led to the discovery of cAMP-dependent protein kinase (protein kinase A, or PKA), which catalyzes the phosphorylation and activation of phosphorylase kinase. This was the first protein kinase cascade or signaling module to be elucidated. The epidermal growth factor receptor-Ras-Raf-MEK-ERK signaling module contains protein-tyrosine, protein-serine/threonine, and dual specificity protein kinases. PKA has served as a prototype of this enzyme family and more is known about this enzyme than any other protein kinase. The inactive PKA holoenzyme consists of two regulatory and two catalytic subunits. After binding four molecules of cAMP, the holoenzyme dissociates into a regulatory subunit dimer (each monomer binds two cAMP) and two free and active catalytic subunits. PKA and all other protein kinase domains have a small amino-terminal lobe and large carboxyterminal lobe as determined by X-ray crystallography. The N-lobe and C-lobe form a cleft that serves as a docking site for MgATP. Nearly all active protein kinases contain a K/E/D/D signature sequence that plays important structural and catalytic roles. Protein kinases contain hydrophobic catalytic and regulatory spines and collateral shell residues that are required to assemble the active enzyme. There are two general kinds of conformational changes associated with most protein kinases. The first conformational change involves the formation of an intact regulatory spine to form an active enzyme. The second conformational change occurs in active kinases as they toggle between open and closed conformations during their catalytic cycles. Because mutations and dysregulation of protein kinases play causal roles in human disease, this family of enzymes has become one of the most important drug targets over the past two decades. Imatinib was approved by the United States FDA for the treatment of chronic myelogenous leukemia in 2001; this small molecule inhibits the BCR-Abl protein kinase oncoprotein that results from the formation of the Philadelphia chromosome. More than two dozen other orally effective mechanism-based small molecule protein kinase inhibitors have been subsequently approved by the FDA. These drugs bind to the ATP-binding site of their target enzymes and extend into nearby hydrophobic pockets. Most of these protein kinase inhibitors prolong survival in cancer patients only weeks or months longer than standard cytotoxic therapies. In contrast, the clinical effectiveness of imatinib against chronic myelogenous leukemia is vastly superior to that of any other targeted protein kinase inhibitor with overall survival lasting a decade or more. However, the near universal and expected development of drug resistance in the treatment of neoplastic disorders requires new approaches to solve this therapeutic challenge. Cancer is the predominant indication for these drugs, but disease targets are increasing. For example, we can expect the approval of new drugs inhibiting other protein kinases in the treatment of illnesses such as hypertension, Parkinson's disease, and autoimmune diseases.

Realizing the Allosteric Potential of the Tetrameric Protein Kinase A RIα Holoenzyme

PKA holoenzymes containing two catalytic (C) subunits and a regulatory (R) subunit dimer are activated cooperatively by cAMP. While cooperativity involves the two tandem cAMP binding domains in each R-subunit, additional cooperativity is associated with the tetramer. Of critical importance is the flexible linker in R that contains an inhibitor site (IS). While the IS becomes ordered in the R:C heterodimer, the overall conformation of the tetramer is mediated largely by the N-Linker that connects theD/D domain to the IS. To understand how the N-Linker contributes to assembly of tetrameric holoenzymes, we engineered a monomeric RIα that contains most of the N-Linker, RIα(73-244), and crystallized a holoenzyme complex. Part of the N-linker is now ordered by interactions with a symmetry-related dimer. This complex of two symmetry-related dimers forms a tetramer that reveals novel mechanisms for allosteric regulation and has many features associated with full-length holoenzyme. A model of the tetrameric holoenzyme, based on this structure, is consistent with previous small angle X-ray and neutron scattering data, and is validated with new SAXS data and with an RIα mutation localized to a novel interface unique to the tetramer.

1H, 13C, 15N assignments of the dimeric regulatory subunit (ilvN) of the E. coli AHAS I

Acetohydroxyacid synthase (AHAS) is an enzyme involved in the biosynthesis of the branched chain amino acids viz, valine, leucine and isoleucine. The activity of this enzyme is regulated through feedback inhibition by the end products of the pathway. Here we report the backbone and side-chain assignments of ilvN, the 22kDa dimeric regulatory subunit of E. coli AHAS isoenzyme I, in the valine bound form. Detailed analysis of the structure of ilvN and its interactions with the catalytic subunit of E. coli AHAS I will help in understanding the mechanism of activation and regulation of the branched chain amino acid biosynthesis.

PAF-AH catalytic subunits modulate the Wnt pathway in developing GABAergic neurons

Platelet-activating factor acetylhydrolase 1B (PAF-AH) inactivates the potent phospholipid platelet-activating factor (PAF) and is composed of two catalytic subunits (α1 and α2) and a dimeric regulatory subunit, LIS1. The function of the catalytic subunits in brain development remains unknown. Here we examined their effects on proliferation in the ganglionic eminences and tangential migration. In α1 and α2 catalytic subunits knockout mice we noticed an increase in the size of the ganglionic eminences resulting from increased proliferation of GABAergic neurons. Our results indicate that the catalytic subunits act as negative regulators of the Wnt signaling pathway. Overexpression of each of the PAF-AH catalytic subunits reduced the amount of nuclear beta-catenin and provoked a shift of this protein from the nucleus to the cytoplasm. In the double mutant mice, Wnt signaling increased in the ganglionic eminences and in the dorsal part of the cerebral cortex. In situ hybridization revealed increased and expanded expression of a downstream target of the Wnt pathway (Cyclin D1), and of upstream Wnt components (Tcf4, Tcf3 and Wnt7B). Furthermore, the interneurons in the cerebral cortex were more numerous and in a more advanced position. Transplantation assays revealed a non-cell autonomous component to this phenotype, which may be explained in part by increased and expanded expression of Sdf1 and Netrin-1. Our findings strongly suggest that PAF-AH catalytic subunits modulate the Wnt pathway in restricted areas of the developing cerebral cortex. We hypothesize that modulation of the Wnt pathway is the evolutionary conserved activity of the PAF-AH catalytic subunits.