1
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Venkatakrishnan V, Ghode A, Tulsian NK, Anand GS. Impaired cAMP processivity by phosphodiesterase-protein kinase A complexes in acrodysostosis. Front Mol Biosci 2023; 10:1202268. [PMID: 37808519 PMCID: PMC10552185 DOI: 10.3389/fmolb.2023.1202268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Acrodysostosis represents a group of rare genetic disorders characterized by defective skeletal development and is often accompanied by intellectual disabilities. Mutations in the 3'5'cyclic AMP (cAMP)-dependent protein kinase (PKA) type I regulatory subunit isoform α (RIα) and phosphodiesterase (PDE) PDE4D have both been implicated in impaired PKA regulation in acrodysostosis. How mutations on PDEs and RIα interfere with the regulation of cAMP-PKA signaling is not understood. cAMP-PKA signaling can be described in two phases. In the activation phase, cAMP binding to RIα dissociates the free C-subunit (Catalytic subunit). PDEs hydrolyze cAMP bound to RIα, priming the cAMP-free RIα for reassociation with the C-subunit, thereby completing one PKA activation cycle. Signal termination is thus critical for resetting PKA to its basal state and promoting adaptation to hormonal hyperstimulation. This proceeds through formation of a transient signal termination RIα: PDE complex that facilitates cAMP channeling from the cAMP-binding domain of RIα to the catalytic site of PDE. Signal termination of cAMP-PKA proceeds in three steps: Step 1) Channeling: translocation of cAMP from the CNB of RIα to the PDE catalytic site for hydrolysis. Step 2) Processivity: binding of free cAMP from the cytosol at both CNBs of RIα. Step 3) Product (5'AMP) release from the PDE hydrolysis site through competitive displacement by a new molecule of cAMP that triggers subsequent activation cycles of PKA. We have identified the molecular basis for two acrodysostosis mutants, PDE (PDE8 T690P) and RIα (T207A), that both allosterically impair cAMP-PKA signal termination. A combination of amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and fluorescence polarization (FP) reveals that PDE8 T690P and RIα T207A both blocked processive hydrolysis of cAMP by interfering with competitive displacement of product 5'AMP release from the nucleotide channel at the end of each round of cAMP hydrolysis. While T690P blocked product 5'AMP release from the PDE, T207A greatly slowed the release of the substrate from RIα. These results highlight the role of processivity in cAMP hydrolysis by RIα: PDE termination complexes for adaptation to cAMP from GPCR hyperstimulation. Impairment of the signal termination process provides an alternate molecular basis for acrodysostosis.
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Affiliation(s)
- Varun Venkatakrishnan
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Abhijeet Ghode
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Nikhil K. Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ganesh S. Anand
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
- The Huck Institutes of the life sciences, Pennsylvania State University, University Park, PA, United States
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2
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Role of Protein Kinase A Activation in the Immune System with an Emphasis on Lipopolysaccharide-Responsive and Beige-like Anchor Protein in B Cells. Int J Mol Sci 2023; 24:ijms24043098. [PMID: 36834508 PMCID: PMC9962394 DOI: 10.3390/ijms24043098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/08/2023] Open
Abstract
Cyclic AMP-dependent protein kinase A (PKA) is a ubiquitous enzymatic complex that is involved in a broad spectrum of intracellular receptor signaling. The activity of PKA depends on A-kinase anchoring proteins (AKAPs) that attach to PKAs close to their substrates to control signaling. Although the relevance of PKA-AKAP signaling in the immune system is evident in T cells, its relevance in B and other immune cells remains relatively unclear. In the last decade, lipopolysaccharide-responsive and beige-like anchor protein (LRBA) has emerged as an AKAP that is ubiquitously expressed in B and T cells, specifically after activation. A deficiency of LRBA leads to immune dysregulation and immunodeficiency. The cellular mechanisms regulated by LRBA have not yet been investigated. Therefore, this review summarizes the functions of PKA in immunity and provides the most recent information regarding LRBA deficiency to deepen our understanding of immune regulation and immunological diseases.
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3
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Ando T. Functional Implications of Dynamic Structures of Intrinsically Disordered Proteins Revealed by High-Speed AFM Imaging. Biomolecules 2022; 12:biom12121876. [PMID: 36551304 PMCID: PMC9776203 DOI: 10.3390/biom12121876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The unique functions of intrinsically disordered proteins (IDPs) depend on their dynamic protean structure that often eludes analysis. High-speed atomic force microscopy (HS-AFM) can conduct this difficult analysis by directly visualizing individual IDP molecules in dynamic motion at sub-molecular resolution. After brief descriptions of the microscopy technique, this review first shows that the intermittent tip-sample contact does not alter the dynamic structure of IDPs and then describes how the number of amino acids contained in a fully disordered region can be estimated from its HS-AFM images. Next, the functional relevance of a dumbbell-like structure that has often been observed on IDPs is discussed. Finally, the dynamic structural information of two measles virus IDPs acquired from their HS-AFM and NMR analyses is described together with its functional implications.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
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4
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Thomas R, Hernandez A, Benavides DR, Li W, Tan C, Umfress A, Plattner F, Chakraborti A, Pozzo-Miller L, Taylor SS, Bibb JA. Integrated regulation of PKA by fast and slow neurotransmission in the nucleus accumbens controls plasticity and stress responses. J Biol Chem 2022; 298:102245. [PMID: 35835216 PMCID: PMC9386499 DOI: 10.1016/j.jbc.2022.102245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/30/2022] Open
Abstract
Cortical glutamate and midbrain dopamine neurotransmission converge to mediate striatum-dependent behaviors, while maladaptations in striatal circuitry contribute to mental disorders. However, the crosstalk between glutamate and dopamine signaling has not been entirely elucidated. Here we uncover a molecular mechanism by which glutamatergic and dopaminergic signaling integrate to regulate cAMP-dependent protein kinase (PKA) via phosphorylation of the PKA regulatory subunit, RIIβ. Using a combination of biochemical, pharmacological, neurophysiological, and behavioral approaches, we find that glutamate-dependent reduction in cyclin-dependent kinase 5 (Cdk5)-dependent RIIβ phosphorylation alters the PKA holoenzyme autoinhibitory state to increase PKA signaling in response to dopamine. Furthermore, we show that disruption of RIIβ phosphorylation by Cdk5 enhances cortico-ventral striatal synaptic plasticity. In addition, we demonstrate that acute and chronic stress in rats inversely modulate RIIβ phosphorylation and ventral striatal infusion of a small interfering peptide that selectively targets RIIβ regulation by Cdk5 improves behavioral response to stress. We propose this new signaling mechanism integrating ventral striatal glutamate and dopamine neurotransmission is important to brain function, may contribute to neuropsychiatric conditions, and serves as a possible target for the development of novel therapeutics for stress-related disorders.
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Affiliation(s)
- Rachel Thomas
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104 USA; Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adan Hernandez
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Santiago de Querétaro, Querétaro, México; Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David R Benavides
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wei Li
- Department of Neurobiology, Civitan International Research Center, The University of Alabama Birmingham Medical Center, Birmingham, AL 35233, USA
| | - Chunfeng Tan
- Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030; Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alan Umfress
- Department of Surgery, The University of Alabama Birmingham Medical Center, Birmingham, AL 35233, USA
| | - Florian Plattner
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ayanabha Chakraborti
- Department of Surgery, The University of Alabama Birmingham Medical Center, Birmingham, AL 35233, USA
| | - Lucas Pozzo-Miller
- Department of Neurobiology, Civitan International Research Center, The University of Alabama Birmingham Medical Center, Birmingham, AL 35233, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - James A Bibb
- Department of Neurobiology, Civitan International Research Center, The University of Alabama Birmingham Medical Center, Birmingham, AL 35233, USA; Department of Surgery, The University of Alabama Birmingham Medical Center, Birmingham, AL 35233, USA; Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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5
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Roa JN, Ma Y, Mikulski Z, Xu Q, Ilouz R, Taylor SS, Skowronska-Krawczyk D. Protein Kinase A in Human Retina: Differential Localization of Cβ, Cα, RIIα, and RIIβ in Photoreceptors Highlights Non-redundancy of Protein Kinase A Subunits. Front Mol Neurosci 2021; 14:782041. [PMID: 34867193 PMCID: PMC8636463 DOI: 10.3389/fnmol.2021.782041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Protein kinase A (PKA) signaling is essential for numerous processes but the subcellular localization of specific PKA regulatory (R) and catalytic (C) subunits has yet to be explored comprehensively. Additionally, the localization of the Cβ subunit has never been spatially mapped in any tissue even though ∼50% of PKA signaling in neuronal tissues is thought to be mediated by Cβ. Here we used human retina with its highly specialized neurons as a window into PKA signaling in the brain and characterized localization of PKA Cα, Cβ, RIIα, and RIIβ subunits. We found that each subunit presented a distinct localization pattern. Cα and Cβ were localized in all cell layers (photoreceptors, interneurons, retinal ganglion cells), while RIIα and RIIβ were selectively enriched in photoreceptor cells where both showed distinct patterns of co-localization with Cα but not Cβ. Only Cα was observed in photoreceptor outer segments and at the base of the connecting cilium. Cβ in turn, was highly enriched in mitochondria and was especially prominent in the ellipsoid of cone cells. Further investigation of Cβ using RNA BaseScope technology showed that two Cβ splice variants (Cβ4 and Cβ4ab) likely code for the mitochondrial Cβ proteins. Overall, our data indicates that PKA Cα, Cβ, RIIα, and RIIβ subunits are differentially localized and are likely functionally non-redundant in the human retina. Furthermore, Cβ is potentially important for mitochondrial-associated neurodegenerative diseases previously linked to PKA dysfunction.
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Affiliation(s)
- Jinae N Roa
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States
| | - Yuliang Ma
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Qianlan Xu
- Department of Physiology and Biophysics and Department of Ophthalmology, Center for Translational Vision Research, University of California, Irvine, Irvine, CA, United States
| | - Ronit Ilouz
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics and Department of Ophthalmology, Center for Translational Vision Research, University of California, Irvine, Irvine, CA, United States
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6
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Intrinsic disorder in protein kinase A anchoring proteins signaling complexes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021. [PMID: 34656331 DOI: 10.1016/bs.pmbts.2021.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Protein kinase A (PKA) is regulated by a diverse class of anchoring proteins known as AKAPs that target PKA to subsets of its activators and substrates. Recently, it was reported that PKA can remain bound to its regulatory subunit after activation in contrast to classical model of activation-by-dissociation. This implies that PKA remains bound to the AKAPs and its substrates, and thus suggest many phosphorylation reactions occur while PKA is physically connected to its substrate. Intra-complex reactions are sensitive to the architecture of the signaling complex, but generally concentration independent. We show that most AKAPs have long intrinsically disordered regions, and suggest that they represent an adaptation for intra-complex phosphorylation. Based on polymer models of the disordered proteins, we predict that the effective concentrations of tethered substrates range from the low millimolar range to tens of micromolar. Based on recent models for intra-complex enzyme reactions, we suggest that the structure of the AKAP signaling complex is likely to be source of allosteric regulation of PKA signaling.
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7
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Taylor SS, Wu J, Bruystens JGH, Del Rio JC, Lu TW, Kornev AP, Ten Eyck LF. From structure to the dynamic regulation of a molecular switch: A journey over 3 decades. J Biol Chem 2021; 296:100746. [PMID: 33957122 PMCID: PMC8144671 DOI: 10.1016/j.jbc.2021.100746] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
It is difficult to imagine where the signaling community would be today without the Protein Data Bank. This visionary resource, established in the 1970s, has been an essential partner for sharing information between academics and industry for over 3 decades. We describe here the history of our journey with the protein kinases using cAMP-dependent protein kinase as a prototype. We summarize what we have learned since the first structure, published in 1991, why our journey is still ongoing, and why it has been essential to share our structural information. For regulation of kinase activity, we focus on the cAMP-binding protein kinase regulatory subunits. By exploring full-length macromolecular complexes, we discovered not only allostery but also an essential motif originally attributed to crystal packing. Massive genomic data on disease mutations allows us to now revisit crystal packing as a treasure chest of possible protein:protein interfaces where the biological significance and disease relevance can be validated. It provides a new window into exploring dynamic intrinsically disordered regions that previously were deleted, ignored, or attributed to crystal packing. Merging of crystallography with cryo-electron microscopy, cryo-electron tomography, NMR, and millisecond molecular dynamics simulations is opening a new world for the signaling community where those structure coordinates, deposited in the Protein Data Bank, are just a starting point!
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California at San Diego, San Diego, California, USA; Department of Chemistry and Biochemistry, University of California at San Diego, San Diego, California, USA.
| | - Jian Wu
- Department of Pharmacology, University of California at San Diego, San Diego, California, USA
| | - Jessica G H Bruystens
- Department of Pharmacology, University of California at San Diego, San Diego, California, USA
| | - Jason C Del Rio
- Department of Pharmacology, University of California at San Diego, San Diego, California, USA
| | - Tsan-Wen Lu
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, San Diego, California, USA
| | - Lynn F Ten Eyck
- Department of Chemistry and Biochemistry, University of California at San Diego, San Diego, California, USA; San Diego Supercomputer Center, University of California at San Diego, San Diego, California, USA
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8
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Baro Graf C, Ritagliati C, Stival C, Luque GM, Gentile I, Buffone MG, Krapf D. Everything you ever wanted to know about PKA regulation and its involvement in mammalian sperm capacitation. Mol Cell Endocrinol 2020; 518:110992. [PMID: 32853743 DOI: 10.1016/j.mce.2020.110992] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022]
Abstract
The 3', 5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase (PKA) is a tetrameric holoenzyme comprising a set of two regulatory subunits (PKA-R) and two catalytic (PKA-C) subunits. The PKA-R subunits act as sensors of cAMP and allow PKA-C activity. One of the first signaling events observed during mammalian sperm capacitation is PKA activation. Thus, understanding how PKA activity is restricted in space and time is crucial to decipher the critical steps of sperm capacitation. It is widely accepted that PKA specificity depends on several levels of regulation. Anchoring proteins play a pivotal role in achieving proper localization signaling, subcellular targeting and cAMP microdomains. These multi-factorial regulation steps are necessary for a precise spatio-temporal activation of PKA. Here we discuss recent understanding of regulatory mechanisms of PKA in mammalian sperm, such as post-translational modifications, in the context of its role as the master orchestrator of molecular events conducive to capacitation.
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Affiliation(s)
- Carolina Baro Graf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina; Laboratorio de Medicina Reproductiva (LMR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Carla Ritagliati
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Cintia Stival
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Guillermina M Luque
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Iñaki Gentile
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina
| | - Mariano G Buffone
- Laboratory of Cellular and Molecular Reproductive Biology, Instituto de Biología y Medicina Experimental (IBYME), CONICET, Buenos Aires, Argentina
| | - Dario Krapf
- Laboratory of Cell Signal Transduction Networks, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-UNR, Rosario, Argentina; Laboratorio de Medicina Reproductiva (LMR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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9
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Switching of the folding-energy landscape governs the allosteric activation of protein kinase A. Proc Natl Acad Sci U S A 2018; 115:E7478-E7485. [PMID: 30038016 DOI: 10.1073/pnas.1802510115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are dynamic molecular switches that sample multiple conformational states. The regulatory subunit of PKA harbors two cAMP-binding domains [cyclic nucleotide-binding (CNB) domains] that oscillate between inactive and active conformations dependent on cAMP binding. The cooperative binding of cAMP to the CNB domains activates an allosteric interaction network that enables PKA to progress from the inactive to active conformation, unleashing the activity of the catalytic subunit. Despite its importance in the regulation of many biological processes, the molecular mechanism responsible for the observed cooperativity during the activation of PKA remains unclear. Here, we use optical tweezers to probe the folding cooperativity and energetics of domain communication between the cAMP-binding domains in the apo state and bound to the catalytic subunit. Our study provides direct evidence of a switch in the folding-energy landscape of the two CNB domains from energetically independent in the apo state to highly cooperative and energetically coupled in the presence of the catalytic subunit. Moreover, we show that destabilizing mutational effects in one CNB domain efficiently propagate to the other and decrease the folding cooperativity between them. Taken together, our results provide a thermodynamic foundation for the conformational plasticity that enables protein kinases to adapt and respond to signaling molecules.
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10
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Haushalter KJ, Casteel DE, Raffeiner A, Stefan E, Patel HH, Taylor SS. Phosphorylation of protein kinase A (PKA) regulatory subunit RIα by protein kinase G (PKG) primes PKA for catalytic activity in cells. J Biol Chem 2018; 293:4411-4421. [PMID: 29378851 PMCID: PMC5868259 DOI: 10.1074/jbc.m117.809988] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/23/2018] [Indexed: 01/26/2023] Open
Abstract
cAMP-dependent protein kinase (PKAc) is a pivotal signaling protein in eukaryotic cells. PKAc has two well-characterized regulatory subunit proteins, RI and RII (each having α and β isoforms), which keep the PKAc catalytic subunit in a catalytically inactive state until activation by cAMP. Previous reports showed that the RIα regulatory subunit is phosphorylated by cGMP-dependent protein kinase (PKG) in vitro, whereupon phosphorylated RIα no longer inhibits PKAc at normal (1:1) stoichiometric ratios. However, the significance of this phosphorylation as a mechanism for activating type I PKA holoenzymes has not been fully explored, especially in cellular systems. In this study, we further examined the potential of RIα phosphorylation to regulate physiologically relevant "desensitization" of PKAc activity. First, the serine 101 site of RIα was validated as a target of PKGIα phosphorylation both in vitro and in cells. Analysis of a phosphomimetic substitution in RIα (S101E) showed that modification of this site increases PKAc activity in vitro and in cells, even without cAMP stimulation. Numerous techniques were used to show that although Ser101 variants of RIα can bind PKAc, the modified linker region of the S101E mutant has a significantly reduced affinity for the PKAc active site. These findings suggest that RIα phosphorylation may be a novel mechanism to circumvent the requirement of cAMP stimulus to activate type I PKA in cells. We have thus proposed a model to explain how PKG phosphorylation of RIα creates a "sensitized intermediate" state that is in effect primed to trigger PKAc activity.
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Affiliation(s)
| | | | - Andrea Raffeiner
- the Institute of Biochemistry, University of Innsbruck, A-6020 Innsbruck, Austria, and
| | - Eduard Stefan
- the Institute of Biochemistry, University of Innsbruck, A-6020 Innsbruck, Austria, and
| | - Hemal H Patel
- Anesthesiology, and
- the Veterans Affairs San Diego Healthcare System, San Diego, California 92161
| | - Susan S Taylor
- From the Departments of Chemistry & Biochemistry,
- Pharmacology, University of California, San Diego, La Jolla, California 92093-0654
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11
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Wild AR, Dell'Acqua ML. Potential for therapeutic targeting of AKAP signaling complexes in nervous system disorders. Pharmacol Ther 2017; 185:99-121. [PMID: 29262295 DOI: 10.1016/j.pharmthera.2017.12.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A common feature of neurological and neuropsychiatric disorders is a breakdown in the integrity of intracellular signal transduction pathways. Dysregulation of ion channels and receptors in the cell membrane and the enzymatic mediators that link them to intracellular effectors can lead to synaptic dysfunction and neuronal death. However, therapeutic targeting of these ubiquitous signaling elements can lead to off-target side effects due to their widespread expression in multiple systems of the body. A-kinase anchoring proteins (AKAPs) are multivalent scaffolding proteins that compartmentalize a diverse range of receptor and effector proteins to streamline signaling within nanodomain signalosomes. A number of essential neurological processes are known to critically depend on AKAP-directed signaling and an understanding of the role AKAPs play in nervous system disorders has emerged in recent years. Selective targeting of AKAP protein-protein interactions may be a means to uncouple pathologically active signaling pathways in neurological disorders with a greater degree of specificity. In this review we will discuss the role of AKAPs in both regulating normal nervous system function and dysfunction associated with disease, and the potential for therapeutic targeting of AKAP signaling complexes.
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Affiliation(s)
- Angela R Wild
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mark L Dell'Acqua
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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12
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Hirakis SP, Malmstrom RD, Amaro RE. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry 2017; 56:3885-3888. [PMID: 28661131 PMCID: PMC5751417 DOI: 10.1021/acs.biochem.7b00461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We identify a previously unresolved, unrecognized, and highly stable conformation of the protein kinase A (PKA) regulatory subunit RIα. This conformation, which we term the "Flipback" structure, bridges conflicting characteristics in crystallographic structures and solution experiments of the PKA RIα heterotetramer. Our simulations reveal a hinge residue, G235, in the B/C helix that is conserved through all isoforms of RI. Brownian dynamics simulations suggest that the Flipback conformation plays a role in cAMP association to the A domain of the R subunit.
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Affiliation(s)
- Sophia P. Hirakis
- Department of Chemistry and Biochemistry and National Biomedical Computational Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Robert D. Malmstrom
- Department of Chemistry and Biochemistry and National Biomedical Computational Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry and National Biomedical Computational Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0304
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13
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Melville Z, Hernández-Ochoa EO, Pratt SJP, Liu Y, Pierce AD, Wilder PT, Adipietro KA, Breysse DH, Varney KM, Schneider MF, Weber DJ. The Activation of Protein Kinase A by the Calcium-Binding Protein S100A1 Is Independent of Cyclic AMP. Biochemistry 2017; 56:2328-2337. [PMID: 28409622 PMCID: PMC5415871 DOI: 10.1021/acs.biochem.7b00117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Biochemical
and structural studies demonstrate that S100A1 is involved
in a Ca2+-dependent interaction with the type 2α
and type 2β regulatory subunits of protein kinase A (PKA) (RIIα
and RIIβ) to activate holo-PKA. The interaction was specific
for S100A1 because other calcium-binding proteins (i.e., S100B and
calmodulin) had no effect. Likewise, a role for S100A1
in PKA-dependent signaling was established because the PKA-dependent
subcellular redistribution of HDAC4 was abolished in cells derived
from S100A1 knockout mice. Thus, the Ca2+-dependent interaction
between S100A1 and the type 2 regulatory subunits represents a novel
mechanism that provides a link between Ca2+ and PKA signaling,
which is important for the regulation of gene expression in skeletal
muscle via HDAC4 cytosolic–nuclear trafficking.
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Affiliation(s)
- Zephan Melville
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Erick O Hernández-Ochoa
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Stephen J P Pratt
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Yewei Liu
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Adam D Pierce
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Paul T Wilder
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Kaylin A Adipietro
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Daniel H Breysse
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - Martin F Schneider
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
| | - David J Weber
- Department of Biochemistry and Molecular Biology and ‡Center for Biomolecular Therapeutics, University of Maryland School of Medicine , 108 North Greene Street, Baltimore, Maryland 21201, United States
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14
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Bruystens JG, Wu J, Fortezzo A, Del Rio J, Nielsen C, Blumenthal DK, Rock R, Stefan E, Taylor SS. Structure of a PKA RIα Recurrent Acrodysostosis Mutant Explains Defective cAMP-Dependent Activation. J Mol Biol 2016; 428:4890-4904. [PMID: 27825928 PMCID: PMC5149412 DOI: 10.1016/j.jmb.2016.10.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/08/2016] [Accepted: 10/31/2016] [Indexed: 01/03/2023]
Abstract
Most disease-related mutations that impair cAMP protein kinase A (PKA) signaling are present within the regulatory (R) PKA RI alpha-subunit (RIα). Although mutations in the PRKAR1A gene are linked to Carney complex (CNC) disease and, more recently, to acrodysostosis-1 (ACRDYS1), the two diseases show contrasting phenotypes. While CNC mutations cause increased PKA activity, ACRDYS1 mutations result in decreased PKA activity and cAMP resistant holoenzymes. Mapping the ACRDYS1 disease mutations reveals their localization to the second of two tandem cAMP-binding (CNB) domains (CNB-B), and here, we characterize a recurrent deletion mutant where the last 14 residues are missing. The crystal structure of a monomeric form of this mutant (RIα92-365) bound to the catalytic (C)-subunit reveals the dysfunctional regions of the RIα subunit. Beyond the missing residues, the entire capping motif is disordered (residues 357-379) and explains the disrupted cAMP binding. Moreover, the effects of the mutation extend far beyond the CNB-B domain and include the active site and N-lobe of the C-subunit, which is in a partially open conformation with the C-tail disordered. A key residue that contributes to this crosstalk, D267, is altered in our structure, and we confirmed its functional importance by mutagenesis. In particular, the D267 interaction with Arg241, a residue shown earlier to be important for allosteric regulation, is disrupted, thereby strengthening the interaction of D267 with the C-subunit residue Arg194 at the R:C interface. We see here how the switch between active (cAMP-bound) and inactive (holoenzyme) conformations is perturbed and how the dynamically controlled crosstalk between the helical domains of the two CNB domains is necessary for the functional regulation of PKA activity.
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Affiliation(s)
- Jessica Gh Bruystens
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jian Wu
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Audrey Fortezzo
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jason Del Rio
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Cole Nielsen
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ruth Rock
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
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15
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González Bardeci N, Caramelo JJ, Blumenthal DK, Rinaldi J, Rossi S, Moreno S. The PKA regulatory subunit from yeast forms a homotetramer: Low-resolution structure of the N-terminal oligomerization domain. J Struct Biol 2016; 193:141-54. [DOI: 10.1016/j.jsb.2015.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/13/2015] [Accepted: 12/06/2015] [Indexed: 01/23/2023]
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16
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Nygren PJ, Scott JD. Therapeutic strategies for anchored kinases and phosphatases: exploiting short linear motifs and intrinsic disorder. Front Pharmacol 2015; 6:158. [PMID: 26283967 PMCID: PMC4516873 DOI: 10.3389/fphar.2015.00158] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/16/2015] [Indexed: 12/17/2022] Open
Abstract
Phosphorylation events that occur in response to the second messenger cAMP are controlled spatially and temporally by protein kinase A (PKA) interacting with A-kinase anchoring proteins (AKAPs). Recent advances in understanding the structural basis for this interaction have reinforced the hypothesis that AKAPs create spatially constrained signaling microdomains. This has led to the realization that the PKA/AKAP interface is a potential drug target for modulating a plethora of cell-signaling events. Pharmacological disruption of kinase–AKAP interactions has previously been explored for disease treatment and remains an interesting area of research. However, disrupting or enhancing the association of phosphatases with AKAPs is a therapeutic concept of equal promise, particularly since they oppose the actions of many anchored kinases. Accordingly, numerous AKAPs bind phosphatases such as protein phosphatase 1 (PP1), calcineurin (PP2B), and PP2A. These multimodal signaling hubs are equally able to control the addition of phosphate groups onto target substrates, as well as the removal of these phosphate groups. In this review, we describe recent advances in structural analysis of kinase and phosphatase interactions with AKAPs, and suggest future possibilities for targeting these interactions for therapeutic benefit.
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Affiliation(s)
- Patrick J Nygren
- Department of Pharmacology, University of Washington Seattle, WA, USA ; Howard Hughes Medical Institute Chevy Chase, MD, USA
| | - John D Scott
- Department of Pharmacology, University of Washington Seattle, WA, USA ; Howard Hughes Medical Institute Chevy Chase, MD, USA
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17
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Abstract
cAMP-dependent protein kinase (PKA) was the second protein kinase to be discovered and the PKA catalytic (C) subunit serves as a prototype for the large protein kinase superfamily that contains over 500 gene products. The protein kinases regulate much of biology in eukaryotic cells and they are now also a major therapeutic target. Although PKA was discovered nearly 50 years ago and the subsequent discovery of the regulatory subunits that bind cAMP and release the catalytic activity from the holoenzyme followed quickly. Thus in PKA we see the convergence of two major signaling mechanisms - protein phosphorylation and second messenger signaling through cAMP. Crystallography provides a foundation for understanding function, and the structure of the isolated regulatory (R) and C-subunits have been extremely informative. Yet it is the R2C2 holoenzyme that predominates in cells, and one can only appreciate the allosteric features of PKA signaling by seeing the full length protein. The symmetry and the quaternary constraints that one R:C hetero-dimer exerts on the other in the holoenzyme simply are not present in the isolated subunits or even in the R:C hetero-dimer.
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Affiliation(s)
- Ping Zhang
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Jian Wu
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093 ; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093
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18
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Blumenthal DK, Copps J, Smith-Nguyen EV, Zhang P, Heller WT, Taylor SS. The roles of the RIIβ linker and N-terminal cyclic nucleotide-binding domain in determining the unique structures of the type IIβ protein kinase A: a small angle x-ray and neutron scattering study. J Biol Chem 2014; 289:28505-12. [PMID: 25112875 DOI: 10.1074/jbc.m114.584177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein kinase A (PKA) is ubiquitously expressed and is responsible for regulating many important cellular functions in response to changes in intracellular cAMP concentrations. The PKA holoenzyme is a tetramer (R2:C2), with a regulatory subunit homodimer (R2) that binds and inhibits two catalytic (C) subunits; binding of cAMP to the regulatory subunit homodimer causes activation of the catalytic subunits. Four different R subunit isoforms exist in mammalian cells, and these confer different structural features, subcellular localization, and biochemical properties upon the PKA holoenzymes they form. The holoenzyme containing RIIβ is structurally unique in that the type IIβ holoenzyme is much more compact than the free RIIβ homodimer. We have used small angle x-ray scattering and small angle neutron scattering to study the solution structure and subunit organization of a holoenzyme containing an RIIβ C-terminal deletion mutant (RIIβ(1-280)), which is missing the C-terminal cAMP-binding domain to better understand the structural organization of the type IIβ holoenzyme and the RIIβ domains that contribute to stabilizing the holoenzyme conformation. Our results demonstrate that compaction of the type IIβ holoenzyme does not require the C-terminal cAMP-binding domain but rather involves large structural rearrangements within the linker and N-terminal cyclic nucleotide-binding domain of the RIIβ homodimer. The structural rearrangements are significantly greater than seen previously with RIIα and are likely to be important in mediating short range and long range interdomain and intersubunit interactions that uniquely regulate the activity of the type IIβ isoform of PKA.
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Affiliation(s)
- Donald K Blumenthal
- From the Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah 84112,
| | - Jeffrey Copps
- the Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0654
| | - Eric V Smith-Nguyen
- the Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0654
| | - Ping Zhang
- the Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0654
| | - William T Heller
- the Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and
| | - Susan S Taylor
- the Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0654, the Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0654
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19
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PKA RIα homodimer structure reveals an intermolecular interface with implications for cooperative cAMP binding and Carney complex disease. Structure 2013; 22:59-69. [PMID: 24316401 DOI: 10.1016/j.str.2013.10.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/25/2013] [Accepted: 10/07/2013] [Indexed: 12/31/2022]
Abstract
The regulatory (R) subunit is the cAMP receptor of protein kinase A. Following cAMP binding, the inactive PKA holoenzyme complex separates into two active catalytic (C) subunits and a cAMP-bound R dimer. Thus far, only monomeric R structures have been solved, which fell short in explaining differences of cAMP binding for the full-length protein as compared to the truncated R subunits. Here we solved a full-length R-dimer structure that reflects the biologically relevant conformation, and this structure agrees well with small angle X-ray scattering. An isoform-specific interface is revealed between the protomers. This interface acts as an intermolecular sensor for cAMP and explains the cooperative character of cAMP binding to the RIα dimer. Mutagenesis of residues on this interface not only leads to structural and biochemical changes, but is also linked to Carney complex disease.
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20
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Moon TM, Osborne BW, Dostmann WR. The switch helix: a putative combinatorial relay for interprotomer communication in cGMP-dependent protein kinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1346-51. [PMID: 23416533 DOI: 10.1016/j.bbapap.2013.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/04/2013] [Indexed: 11/26/2022]
Abstract
For over three decades the isozymes of cGMP-dependent protein kinase (PKG) have been studied using an array of biochemical and biophysical techniques. When compared to its closest cousin, cAMP-dependent protein kinase (PKA), these studies revealed a set of identical domain types, yet containing distinct, sequence-specific features. The recently solved structure of the PKG regulatory domain showed the presence of the switch helix (SW), a novel motif that promotes the formation of a domain-swapped dimer in the asymmetric unit. This dimer is mediated by the interaction of a knob motif on the C-terminal locus of the SW, with a hydrophobic nest on the opposing protomer. This nest sits adjacent to the cGMP binding pocket of the B-site. Priming of this site by cGMP may influence the geometry of the hydrophobic nest. Moreover, this unique interaction may have wide implications for the architecture of the inactive and active forms of PKG. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- Thomas M Moon
- Department of Pharmacology, The University of Vermont, Burlington, VT 05405, USA
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21
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Taylor SS, Ilouz R, Zhang P, Kornev AP. Assembly of allosteric macromolecular switches: lessons from PKA. Nat Rev Mol Cell Biol 2012; 13:646-58. [PMID: 22992589 DOI: 10.1038/nrm3432] [Citation(s) in RCA: 333] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein kinases are dynamic molecular switches that have evolved to be only transiently activated. Kinase activity is embedded within a conserved kinase core, which is typically regulated by associated domains, linkers and interacting proteins. Moreover, protein kinases are often tethered to large macromolecular complexes to provide tighter spatiotemporal control. Thus, structural characterization of kinase domains alone is insufficient to explain protein kinase function and regulation in vivo. Recent progress in structural characterization of cyclic AMP-dependent protein kinase (PKA) exemplifies how our knowledge of kinase signalling has evolved by shifting the focus of structural studies from single kinase subunits to macromolecular complexes.
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, 92093-90654, USA.
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22
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Boettcher AJ, Wu J, Kim C, Yang J, Bruystens J, Cheung N, Pennypacker JK, Blumenthal DA, Kornev AP, Taylor SS. Realizing the allosteric potential of the tetrameric protein kinase A RIα holoenzyme. Structure 2011; 19:265-76. [PMID: 21300294 DOI: 10.1016/j.str.2010.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Revised: 11/04/2010] [Accepted: 12/06/2010] [Indexed: 11/18/2022]
Abstract
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 the D/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.
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Affiliation(s)
- Angela J Boettcher
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
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23
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Kronberg F, Giacometti R, Ruiz-Herrera J, Passeron S. Characterization of the regulatory subunit of Yarrowia lipolytica cAMP-dependent protein kinase. Evidences of a monomeric protein. Arch Biochem Biophys 2011; 509:66-75. [DOI: 10.1016/j.abb.2011.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 11/27/2022]
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24
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Cheng CY, Yang J, Taylor SS, Blumenthal DK. Sensing domain dynamics in protein kinase A-I{alpha} complexes by solution X-ray scattering. J Biol Chem 2010; 284:35916-25. [PMID: 19837668 PMCID: PMC2791020 DOI: 10.1074/jbc.m109.059493] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The catalytic (C) and regulatory (R) subunits of protein kinase A are exceptionally dynamic proteins. Interactions between the R- and C-subunits are regulated by cAMP binding to the two cyclic nucleotide-binding domains in the R-subunit. Mammalian cells express four different isoforms of the R-subunit (RIα, RIβ, RIIα, and RIIβ) that all interact with the C-subunit in different ways. Here, we investigate the dynamic behavior of protein complexes between RIα and C-subunits using small angle x-ray scattering. We show that a single point mutation in RIα, R333K (which alters the cAMP-binding properties of Domain B) results in a compact shape compared with the extended shape of the wild-type R·C complex. A double mutant complex that disrupts the interaction site between the C-subunit and Domain B in RIα, RIαABR333K·C(K285P), results in a broader P(r) curve that more closely resembles the P(r) profiles of wild-type complexes. These results together suggest that interactions between RIα Domain B and the C-subunit in the RIα·C complex involve large scale dynamics that can be disrupted by single point mutations in both proteins. In contrast to RIα·C complexes. Domain B in the RIIβ·C heterodimer is not dynamic and is critical for both inhibition and complex formation. Our study highlights the functional differences of domain dynamics between protein kinase A isoforms, providing a framework for elucidating the global organization of each holoenzyme and the cross-talk between the R- and C-subunits.
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Affiliation(s)
- Cecilia Y Cheng
- Departments of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92037-0654, USA
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25
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Brown SHJ, Wu J, Kim C, Alberto K, Taylor SS. Novel isoform-specific interfaces revealed by PKA RIIbeta holoenzyme structures. J Mol Biol 2009; 393:1070-82. [PMID: 19748511 DOI: 10.1016/j.jmb.2009.09.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 09/04/2009] [Accepted: 09/08/2009] [Indexed: 11/26/2022]
Abstract
The cAMP-dependent protein kinase catalytic (C) subunit is inhibited by two classes of functionally nonredundant regulatory (R) subunits, RI and RII. Unlike RI subunits, RII subunits are both substrates and inhibitors. Because RIIbeta knockout mice have important disease phenotypes, the RIIbeta holoenzyme is a target for developing isoform-specific agonists and/or antagonists. We also know little about the linker region that connects the inhibitor site to the N-terminal dimerization domain, although this linker determines the unique globular architecture of the RIIbeta holoenzyme. To understand how RIIbeta functions as both an inhibitor and a substrate and to elucidate the structural role of the linker, we engineered different RIIbeta constructs. In the absence of nucleotide, RIIbeta(108-268), which contains a single cyclic nucleotide binding domain, bound C subunit poorly, whereas with AMP-PNP, a non-hydrolyzable ATP analog, the affinity was 11 nM. The RIIbeta(108-268) holoenzyme structure (1.62 A) with AMP-PNP/Mn(2+) showed that we trapped the RIIbeta subunit in an enzyme:substrate complex with the C subunit in a closed conformation. The enhanced affinity afforded by AMP-PNP/Mn(2+) may be a useful strategy for increasing affinity and trapping other protein substrates with their cognate protein kinase. Because mutagenesis predicted that the region N-terminal to the inhibitor site might dock differently to RI and RII, we also engineered RIIbeta(102-265), which contained six additional linker residues. The additional linker residues in RIIbeta(102-265) increased the affinity to 1.6 nM, suggesting that docking to this surface may also enhance catalytic efficiency. In the corresponding holoenzyme structure, this linker docks as an extended strand onto the surface of the large lobe. This hydrophobic pocket, formed by the alphaF-alphaG loop and conserved in many protein kinases, also provides a docking site for the amphipathic helix of PKI. This novel orientation of the linker peptide provides the first clues as to how this region contributes to the unique organization of the RIIbeta holoenzyme.
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Affiliation(s)
- Simon H J Brown
- Departments of Chemistry/Biochemistry and Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093-0654, USA
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26
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The evolution of guanylyl cyclases as multidomain proteins: conserved features of kinase-cyclase domain fusions. J Mol Evol 2009; 68:587-602. [PMID: 19495554 DOI: 10.1007/s00239-009-9242-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2008] [Accepted: 04/21/2009] [Indexed: 12/30/2022]
Abstract
Guanylyl cyclases (GCs) are enzymes that generate cyclic GMP and regulate different physiologic and developmental processes in a number of organisms. GCs possess sequence similarity to class III adenylyl cyclases (ACs) and are present as either membrane-bound receptor GCs or cytosolic soluble GCs. We sought to determine the evolution of GCs using a large-scale bioinformatic analysis and found multiple lineage-specific expansions of GC genes in the genomes of many eukaryotes. Moreover, a few GC-like proteins were identified in prokaryotes, which come fused to a number of different domains, suggesting allosteric regulation of nucleotide cyclase activity. Eukaryotic receptor GCs are associated with a kinase homology domain (KHD), and phylogenetic analysis of these proteins suggest coevolution of the KHD and the associated cyclase domain as well as a conservation of the sequence and the size of the linker region between the KHD and the associated cyclase domain. Finally, we also report the existence of mimiviral proteins that contain putative active kinase domains associated with a cyclase domain, which could suggest early evolution of the fusion of these two important domains involved in signal transduction.
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27
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A subunit of protein kinase a regulates growth and differentiation in the fungus Mucor circinelloides. EUKARYOTIC CELL 2009; 8:933-44. [PMID: 19411621 DOI: 10.1128/ec.00026-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cyclic AMP (cAMP)-dependent protein kinase A (PKA) signaling pathway plays a role in regulating development, growth, and virulence in a number of fungi. To determine whether PKA plays a similar function in zygomycete fungi, a mutant of Mucor circinelloides was generated that lacks pkaR1, one of the regulatory subunits of PKA. The mutant showed a reduction in growth and alterations in germination rates, cell volume, germ tube length, and asexual sporulation. The lack of pkaR1 gene resulted in a highly decreased, but not null, cAMP binding activity and in a protein kinase activity that was still dependent on cAMP, although with a higher -/+ cAMP activity ratio, suggesting the existence of other cAMP binding activities. Consequently, three proteins analogous to pkaR1 were predicted from the recently sequenced genome of M. circinelloides and were named pkaR2, pkaR3, and pkaR4. Two of the proteins, pkaR2 and pkaR3, with cAMP binding activity were isolated from the wild-type strain and identified by mass spectrometry. The expression of all genes was detected at the mRNA level by semiquantitative reverse transcription-PCR, and they showed a differential expression at different developmental stages. This is the first time that a fungus is reported to have more than one gene encoding the regulatory subunit of PKA.
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28
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Bertinetti D, Schweinsberg S, Hanke SE, Schwede F, Bertinetti O, Drewianka S, Genieser HG, Herberg FW. Chemical tools selectively target components of the PKA system. BMC CHEMICAL BIOLOGY 2009; 9:3. [PMID: 19216744 PMCID: PMC2660902 DOI: 10.1186/1472-6769-9-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 02/12/2009] [Indexed: 11/23/2022]
Abstract
Background In the eukaryotic cell the cAMP-dependent protein kinase (PKA) is a key enzyme in signal transduction and represents the main target of the second messenger cAMP. Here we describe the design, synthesis and characterisation of specifically tailored cAMP analogs which can be utilised as a tool for affinity enrichment and purification as well as for proteomics based analyses of cAMP binding proteins. Results Two sets of chemical binders were developed based on the phosphorothioate derivatives of cAMP, Sp-cAMPS and Rp-cAMPS acting as cAMP-agonists and -antagonists, respectively. These compounds were tested via direct surface plasmon resonance (SPR) analyses for their binding properties to PKA R-subunits and holoenzyme. Furthermore, these analogs were used in an affinity purification approach to analyse their binding and elution properties for the enrichment and improvement of cAMP binding proteins exemplified by the PKA R-subunits. As determined by SPR, all tested Sp-analogs provide valuable tools for affinity chromatography. However, Sp-8-AEA-cAMPS displayed (i) superior enrichment properties while maintaining low unspecific binding to other proteins in crude cell lysates, (ii) allowing mild elution conditions and (iii) providing the capability to efficiently purify all four isoforms of active PKA R-subunit in milligram quantities within 8 h. In a chemical proteomics approach both sets of binders, Rp- and Sp-cAMPS derivatives, can be employed. Whereas Sp-8-AEA-cAMPS preferentially binds free R-subunit, Rp-AHDAA-cAMPS, displaying antagonist properties, not only binds to the free PKA R-subunits but also to the intact PKA holoenzyme both from recombinant and endogenous sources. Conclusion In summary, all tested cAMP analogs were useful for their respective application as an affinity reagent which can enhance purification of cAMP binding proteins. Sp-8-AEA-cAMPS was considered the most efficient analog since Sp-8-AHA-cAMPS and Sp-2-AHA-cAMPS, demonstrated incomplete elution from the matrix, as well as retaining notable amounts of bound protein contaminants. Furthermore it could be demonstrated that an affinity resin based on Rp-8-AHDAA-cAMPS provides a valuable tool for chemical proteomics approaches.
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Affiliation(s)
- Daniela Bertinetti
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Sonja Schweinsberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Susanne E Hanke
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Frank Schwede
- Biolog Life Science Institute, Flughafendamm 9a, P.O. Box 107125, Bremen, Germany
| | - Oliver Bertinetti
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | | | | | - Friedrich W Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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29
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de Piña MZ, Vázquez-Meza H, Pardo JP, Rendón JL, Villalobos-Molina R, Riveros-Rosas H, Piña E. Signaling the signal, cyclic AMP-dependent protein kinase inhibition by insulin-formed H2O2 and reactivation by thioredoxin. J Biol Chem 2008; 283:12373-86. [PMID: 18326045 DOI: 10.1074/jbc.m706832200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catecholamines in adipose tissue promote lipolysis via cAMP, whereas insulin stimulates lipogenesis. Here we show that H(2)O(2) generated by insulin in rat adipocytes impaired cAMP-mediated amplification cascade of lipolysis. These micromolar concentrations of H(2)O(2) added before cAMP suppressed cAMP activation of type IIbeta cyclic AMP-dependent protein kinase (PKA) holoenzyme, prevented hormone-sensitive lipase translocation from cytosol to storage droplets, and inhibited lipolysis. Similarly, H(2)O(2) impaired activation of type IIalpha PKA holoenzyme from bovine heart and from that reconstituted with regulatory IIalpha and catalytic alpha subunits. H(2)O(2) was ineffective (a) if these PKA holoenzymes were preincubated with cAMP, (b) if added to the catalytic alpha subunit, which is active independently of cAMP activation, and (c) if the catalytic alpha subunit was substituted by its C199A mutant in the reconstituted holoenzyme. H(2)O(2) inhibition of PKA activation remained after H(2)O(2) elimination by gel filtration but was reverted with dithiothreitol or with thioredoxin reductase plus thioredoxin. Electrophoresis of holoenzyme in SDS gels showed separation of catalytic and regulatory subunits after cAMP incubation but a single band after H(2)O(2) incubation. These data strongly suggest that H(2)O(2) promotes the formation of an intersubunit disulfide bond, impairing cAMP-dependent PKA activation. Phylogenetic analysis showed that Cys-97 is conserved only in type II regulatory subunits and not in type I regulatory subunits; hence, the redox regulation mechanism described is restricted to type II PKA-expressing tissues. In conclusion, phylogenetic analysis results, selective chemical behavior, and the privileged position in holoenzyme lead us to suggest that Cys-97 in regulatory IIalpha or IIbeta subunits is the residue forming the disulfide bond with Cys-199 in the PKA catalytic alpha subunit. A new molecular point for cross-talk among heterologous signal transduction pathways is demonstrated.
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Affiliation(s)
- Martha Zentella de Piña
- Departamento de Bioquímica, Facultad de Medicina, and Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, México, DF 04510, México
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30
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Chan J, Whitten AE, Jeffries CM, Bosanac I, Mal TK, Ito J, Porumb H, Michikawa T, Mikoshiba K, Trewhella J, Ikura M. Ligand-induced Conformational Changes via Flexible Linkers in the Amino-terminal region of the Inositol 1,4,5-Trisphosphate Receptor. J Mol Biol 2007; 373:1269-80. [PMID: 17915250 DOI: 10.1016/j.jmb.2007.08.057] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Revised: 08/24/2007] [Accepted: 08/24/2007] [Indexed: 11/18/2022]
Abstract
Cytoplasmic Ca2+ signals are highly regulated by various ion transporters, including the inositol 1,4,5-trisphosphate (IP(3)) receptor (IP(3)R), which functions as a Ca2+ release channel on the endoplasmic reticulum membrane. Crystal structures of the two N-terminal regulatory regions from type 1 IP(3)R have been reported; those of the IP(3)-binding core (IP(3)R(CORE)) with bound IP(3), and the suppressor domain. This study examines the structural effects of ligand binding on an IP(3)R construct, designated IP(3)R(N), that contains both the IP(3)-binding core and the suppressor domain. Our circular dichroism results reveal that the IP(3)-bound and IP(3)-free states have similar secondary structure content, consistent with preservation of the overall fold within the individual domains. Thermal denaturation data show that, while IP(3) has a large effect on the stability of IP(3)R(CORE), it has little effect on IP(3)R(N), indicating that the suppressor domain is critical to the stability of IP(3)R(N). The NMR data for IP(3)R(N) provide evidence for chemical exchange, which may be due to protein conformational dynamics in both apo and IP(3)-bound states: a conclusion supported by the small-angle X-ray scattering data. Further, the scattering data show that IP(3)R(N) undergoes a change in average conformation in response to IP(3) binding and the presence of Ca2+ in the solution. Taken together, these data lead us to propose that there are two flexible linkers in the N-terminal region of IP(3)R that join stably folded domains and give rise to an equilibrium mixture of conformational sub-states containing compact and more extended structures. IP(3) binding drives the conformational equilibrium toward more compact structures, while the presence of Ca2+ drives it to a more extended set.
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Affiliation(s)
- Jenny Chan
- Division of Signaling Biology, Ontario Cancer Institute, Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1L7
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31
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Wu J, Brown SHJ, von Daake S, Taylor SS. PKA type IIalpha holoenzyme reveals a combinatorial strategy for isoform diversity. Science 2007; 318:274-9. [PMID: 17932298 PMCID: PMC4036697 DOI: 10.1126/science.1146447] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The catalytic (C) subunit of cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is inhibited by two classes of regulatory subunits, RI and RII. The RII subunits are substrates as well as inhibitors and do not require adenosine triphosphate (ATP) to form holoenzyme, which distinguishes them from RI subunits. To understand the molecular basis for isoform diversity, we solved the crystal structure of an RIIalpha holoenzyme and compared it to the RIalpha holoenzyme. Unphosphorylated RIIalpha(90-400), a deletion mutant, undergoes major conformational changes as both of the cAMP-binding domains wrap around the C subunit's large lobe. The hallmark of this conformational reorganization is the helix switch in domain A. The C subunit is in an open conformation, and its carboxyl-terminal tail is disordered. This structure demonstrates the conserved and isoform-specific features of RI and RII and the importance of ATP, and also provides a new paradigm for designing isoform-specific activators or antagonists for PKA.
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Affiliation(s)
- Jian Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Simon H. J. Brown
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sventja von Daake
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
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32
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Anand GS, Hotchko M, Brown SHJ, Ten Eyck LF, Komives EA, Taylor SS. R-subunit isoform specificity in protein kinase A: distinct features of protein interfaces in PKA types I and II by amide H/2H exchange mass spectrometry. J Mol Biol 2007; 374:487-99. [PMID: 17942118 DOI: 10.1016/j.jmb.2007.09.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 09/07/2007] [Accepted: 09/13/2007] [Indexed: 11/18/2022]
Abstract
The two isoforms (RI and RII) of the regulatory (R) subunit of cAMP-dependent protein kinase or protein kinase A (PKA) are similar in sequence yet have different biochemical properties and physiological functions. To further understand the molecular basis for R-isoform-specificity, the interactions of the RIIbeta isoform with the PKA catalytic (C) subunit were analyzed by amide H/(2)H exchange mass spectrometry to compare solvent accessibility of RIIbeta and the C subunit in their free and complexed states. Direct mapping of the RIIbeta-C interface revealed important differences between the intersubunit interfaces in the type I and type II holoenzyme complexes. These differences are seen in both the R-subunits as well as the C-subunit. Unlike the type I isoform, the type II isoform complexes require both cAMP-binding domains, and ATP is not obligatory for high affinity interactions with the C-subunit. Surprisingly, the C-subunit mediates distinct, overlapping surfaces of interaction with the two R-isoforms despite a strong homology in sequence and similarity in domain organization. Identification of a remote allosteric site on the C-subunit that is essential for interactions with RII, but not RI subunits, further highlights the considerable diversity in interfaces found in higher order protein complexes mediated by the C-subunit of PKA.
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Affiliation(s)
- Ganesh S Anand
- Howard Hughes Medical Institute, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0359, USA
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33
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Ocampo J, Moreno S, Rossi S. PKA from Mucor circinelloides: model to study the role of linker I in the interaction between R and C subunits. Biochem Biophys Res Commun 2007; 362:721-6. [PMID: 17761146 DOI: 10.1016/j.bbrc.2007.08.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/10/2007] [Indexed: 01/14/2023]
Abstract
Protein kinase A from the fungus Mucor circinelloides shows high affinity interaction between regulatory (R) and catalytic (C) subunits. Its R subunit shows a differential presence of several acidic residues in linker I region, in the amino terminus. Mutants R1, lacking the N-terminal region, and R2, lacking the acidic cluster, were used to analyze its effect on the interaction with the C subunit, assessed through inhibition of catalytic activity and cAMP activation of reconstituted holoenzyme. A similar decrease in the interaction was obtained when using R1 and R2 with the homologous C subunit; however when using heterologous bovine C, only R1 had a decreased interaction. The results show the general importance of linker I region in the R-C interaction in protein kinases A and point to the importance of the acidic cluster present in the N-terminus of M. circinelloides R subunit in the high affinity interaction between R and C in this holoenzyme.
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Affiliation(s)
- Josefina Ocampo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y, Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, 1428 Buenos Aires, Argentina
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34
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Diskar M, Zenn HM, Kaupisch A, Prinz A, Herberg FW. Molecular basis for isoform-specific autoregulation of protein kinase A. Cell Signal 2007; 19:2024-34. [PMID: 17614255 DOI: 10.1016/j.cellsig.2007.05.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
Protein kinase A (PKA) isozymes are distinguishable by the inhibitory pattern of their regulatory (R) subunits with RI subunits containing a pseudophosphorylation P(0)-site and RII subunits being a substrate. Under physiological conditions, RII does not inhibit PrKX, the human X chromosome encoded PKA catalytic (C) subunit. Using a live cell Bioluminescence Resonance Energy Transfer (BRET) assay, Surface Plasmon Resonance (SPR) and kinase activity assays, we identified the P(0)-position of the R subunits as the determinant of PrKX autoinhibition. Holoenzyme formation only takes place with an alanine at position P(0), whereas RI subunits containing serine, phosphoserine or aspartate do not bind PrKX. Surprisingly, PrKX reversibly associates with RII when changing P(0) from serine to alanine. In contrast, PKA-Calpha forms holoenzyme complexes with all wildtype and mutant R subunits; however, holoenzyme re-activation by cAMP is severely affected. Only PKA type II or mutant PKA type I holoenzymes (P(0): Ser or Asp) are able to dissociate fully upon maximally elevated intracellular cAMP. The data are of particular significance for understanding PKA isoform-specific activation patterns in living cells.
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Affiliation(s)
- Mandy Diskar
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany.
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35
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Trewhella J. Protein kinase A targeting and activation as seen by small-angle solution scattering. Eur J Cell Biol 2006; 85:655-62. [PMID: 16460833 DOI: 10.1016/j.ejcb.2006.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We have studied the solution structures of the multi-functional protein kinase A using small-angle X-ray and neutron scattering and have found a remarkable structural diversity in the different isoforms of this multi-subunit enzyme, in spite of its having high sequence homology and a common domain organization within its sequences. The available high-resolution crystal and NMR structural data for the protein kinase A components have aided in the interpretation of the solution scattering data and enabled us to develop models that bring insights into protein kinase A activation and targeting mechanisms, such as the opening and closing of the catalytic cleft to facilitate substrate binding or inhibition, respectively, and the role of sequence segments that join functional domains in the R subunit in providing a structurally flexible scaffold for interactions with the C subunit and A kinase-anchoring proteins (AKAPs).
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Affiliation(s)
- Jill Trewhella
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney 2006, NSW, Australia.
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36
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Gibson C, Schanen B, Chakrabarti D, Chakrabarti R. Functional characterisation of the regulatory subunit of cyclic AMP-dependent protein kinase A homologue of Giardia lamblia: Differential expression of the regulatory and catalytic subunits during encystation. Int J Parasitol 2006; 36:791-9. [PMID: 16472811 DOI: 10.1016/j.ijpara.2005.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Revised: 11/19/2005] [Accepted: 11/25/2005] [Indexed: 10/25/2022]
Abstract
To understand the functional roles of protein kinase A (PKA) during vegetative and differentiating states of Giardia parasites, we studied the structural and functional characteristics of the regulatory subunit of PKA (gPKAr) and its involvement in the giardial encystment process. Molecular cloning and characterisation showed that gPKAr contains two tandem 3'5'-cyclic adenosine monphosphate (cyclic AMP) binding domains at the C-terminal end and the interaction domain for the catalytic subunit. A number of consensus residues including in vivo phosphorylation site for PKAc and dimerisation/docking domain are present in gPKAr. The regulatory subunit physically interacts with the catalytic subunit and inhibits its kinase activity in the absence of cyclic AMP, which could be partially restored upon addition of cyclic AMP. Western blot analysis showed a marked reduction in the endogenous gPKAr concentration during differentiation of Giardia into cysts. An increased activity of gPKAc was also detected during encystation without any significant change in the protein concentration. Distinct localisations of gPKAc to the anterior flagella, basal bodies and caudal flagella as noted in trophozoites were absent in encysting cells at later stages. Instead, PKAc staining was punctate and located mostly to the cell periphery. Our study indicates possible enrichment of the active gPKAc during late stages of encystation, which may have implications in completion of the encystment process or priming of cysts for efficient excystation.
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Affiliation(s)
- Candace Gibson
- Department of Molecular Biology and Microbiology, University of Central Florida, 12722 Research Parkway, Orlando, FL 32826, USA
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37
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Kim C, Vigil D, Anand G, Taylor SS. Structure and dynamics of PKA signaling proteins. Eur J Cell Biol 2006; 85:651-4. [PMID: 16647784 DOI: 10.1016/j.ejcb.2006.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Choel Kim
- Department of Chemistry/Biochemistry, Howard Hughes Medical Institute, University of California, Leichtag Biomedical Research Building, Room 412, 9500 Gilman Dr., La Jolla, CA 92093-0654, USA
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38
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Trewhella J. Structural themes and variations in protein kinase A as seen by small-angle scattering and neutron contrast variation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:585-9. [PMID: 16625363 DOI: 10.1007/s00249-006-0061-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Accepted: 03/17/2006] [Indexed: 11/30/2022]
Abstract
Using small-angle solution scattering and neutron contrast variation, we have studied the structure of the multi-subunit protein kinase A. We have gained insights into how nature can take a set of common structural domains (or themes) and modulate their interactions via sequence variations and second messenger mediated signaling to affect enzyme activity and receptor binding important for targeting this multi-function enzyme to specific sub-cellular locations. These studies demonstrate the power of neutron contrast variation to expand our knowledge of the dynamic supra-molecular structures that carry out biological function.
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Affiliation(s)
- Jill Trewhella
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia.
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39
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Gullingsrud J, Kim C, Taylor SS, McCammon JA. Dynamic binding of PKA regulatory subunit RI alpha. Structure 2006; 14:141-9. [PMID: 16407073 DOI: 10.1016/j.str.2005.09.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 09/26/2005] [Accepted: 09/26/2005] [Indexed: 11/24/2022]
Abstract
Recent crystal structures have revealed that regulatory subunit RIalpha of PKA undergoes a dramatic conformational change upon complex formation with the catalytic subunit. Molecular dynamics studies were initiated to elucidate the contributions of intrinsic conformational flexibility and interactions with the catalytic subunit in formation and stabilization of the complex. Simulations of a single RIalpha nucleotide binding domain (NBD), missing cAMP, showed that its C helix spontaneously occupies two distinct conformations: either packed against the nucleotide binding domain as in its cAMP bound structure, or extended into an intermediate form resembling that of the holoenzyme structure. C helix extension was not seen in a simulation of either RIalpha NBD. In a model complex containing both NBDs and the catalytic subunit, well-conserved residues at the interface between the NBDs in the cAMP bound form were found to stabilize the complex through contacts with the catalytic subunit. The model structure is consistent with available experimental data.
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Affiliation(s)
- Justin Gullingsrud
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, USA.
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40
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Vigil D, Blumenthal DK, Taylor SS, Trewhella J. Solution scattering reveals large differences in the global structures of type II protein kinase A isoforms. J Mol Biol 2006; 357:880-9. [PMID: 16460759 DOI: 10.1016/j.jmb.2006.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 12/23/2005] [Accepted: 01/05/2006] [Indexed: 11/17/2022]
Abstract
Isoform diversity within the protein kinase A (PKA) family is achieved by catalytic (C) subunits binding to different isoforms of regulatory subunit homodimers (R2). In a previous small-angle X-ray scattering study, we showed that the type Ialpha R2 homodimer has a distinctive Y-shaped structure, while the IIalpha and IIbeta homodimers are highly flexible and extended in solution. Here we present the results of X-ray scattering experiments on different isoforms of the PKA holoenzyme (R2C2) and show that the type IIbeta R2 homodimer undergoes a dramatic compaction upon binding C subunits that involves a 10A reduction in radius of gyration (from 56 to 46 A) and a 35 A shortening of the maximum linear dimension (from 180-145 A). In contrast, the type IIalpha R2 homodimer shows very little change in these structural parameters and remains extended upon C-subunit binding. This large difference is surprising given the highly conserved sequence and domain organization for the different R isoforms. A mutant RIIbeta holoenzyme and an RIIalpha/RIIbeta chimera were used to explore the role of the sequence linking different functional domains within RIIbeta in the observed C subunit-induced compaction. Structural modeling was used to aid in interpreting the scattering results in terms of the role of inter-domain and inter-subunit contacts in determining the global conformations of the different isoforms. The results provide an important structural foundation for understanding isoform-specific PKA localization and signaling.
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Affiliation(s)
- Dominico Vigil
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92037, USA
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41
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Taylor SS, Kim C, Vigil D, Haste NM, Yang J, Wu J, Anand GS. Dynamics of signaling by PKA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1754:25-37. [PMID: 16214430 DOI: 10.1016/j.bbapap.2005.08.024] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2005] [Revised: 08/11/2005] [Accepted: 08/12/2005] [Indexed: 11/16/2022]
Abstract
The catalytic and regulatory subunits of cAMP-dependent protein kinase (PKA) are highly dynamic signaling proteins. In its dissociated state the catalytic subunit opens and closes as it moves through its catalytic cycle. In this subunit, the core that is shared by all members of the protein kinase family is flanked by N- and C-terminal segments. Each are anchored firmly to the core by well-defined motifs and serve to stabilize the core. Protein kinases are not only catalysts, they are also scaffolds. One of their major functions is to bind to other proteins. In addition to its interactions with the N- and C- termini, the catalytic subunit interacts with its inhibitor proteins, PKI and the regulatory subunits. Both bind with subnanomolar affinity. To achieve this tight binding requires docking of a substrate mimetic to the active site cleft as well as a peripheral docking site. The peripheral site used by PKI is distinct from that used by RIalpha as revealed by a recent structure of a C:RIalpha complex. Upon binding to the catalytic subunit, the linker region of RIalpha becomes ordered. In addition, cAMP-binding domain A undergoes major conformational changes. RIalpha is a highly malleable protein. Using small angle X-ray scattering, the overall shape of the regulatory subunits and corresponding holoenzymes have been elucidated. These studies reveal striking and surprising isoform differences.
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Affiliation(s)
- Susan S Taylor
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry and Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA.
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42
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Vigil D, Blumenthal DK, Taylor SS, Trewhella J. The conformationally dynamic C helix of the RIalpha subunit of protein kinase A mediates isoform-specific domain reorganization upon C subunit binding. J Biol Chem 2005; 280:35521-7. [PMID: 16109722 DOI: 10.1074/jbc.m506769200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Different isoforms of the full-length protein kinase A (PKA) regulatory subunit homodimer (R2) and the catalytic (C) subunit-bound holoenzyme (R2C2) have very different global structures despite similar molecular weights and domain organization within their primary sequences. To date, it has been the linker sequence between the R subunit dimerization/docking domain and cAMP-binding domain A that has been implicated in modulating domain interactions to give rise to these differences in global structure. The small angle solution scattering data presented here for three different isoforms of PKA heterodimer (deltaR-C) complexes reveal a role for another conformationally dynamic sequence in modulating inter-subunit and domain interactions, the C helix that connects the cAMP-binding domains A and B of the R subunit. The deltaR-C heterodimer complexes studied here were each formed with a monomeric N-terminal deletion mutant of the R subunit (deltaR) that contains the inhibitor sequence and both cAMP-binding domains. The scattering data show that type IIalpha and type IIbeta deltaR-C heterodimers are relatively compact and globular, with the C subunit contacting the inhibitor sequence and both cAMP-binding domains. In contrast, the type Ialpha heterodimer is significantly more extended, with the C subunit interacting with the inhibitor sequence and cAMP-binding domain A, whereas domain B extends out such that its surface is almost completely solvent exposed. These data implicate the C helix of RIalpha in modulating isoform-specific interdomain communication in the PKA holoenzyme, adding another layer of structural complexity to our understanding of signaling dynamics in this multisubunit, multidomain protein kinase.
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Affiliation(s)
- Dominico Vigil
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92037, USA
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43
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Pantano S, Zaccolo M, Carloni P. Molecular basis of the allosteric mechanism of cAMP in the regulatory PKA subunit. FEBS Lett 2005; 579:2679-85. [PMID: 15862309 DOI: 10.1016/j.febslet.2005.02.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 02/22/2005] [Accepted: 02/23/2005] [Indexed: 11/20/2022]
Abstract
The second messenger cyclic Adenosine MonoPosphate (cAMP) mediates many biological process by interacting with structurally conserved nucleotide binding domains (cNBD's). Here, we use molecular dynamics simulations on RIIbeta-PKA, one of the best characterized members of the cNBD family, in presence and absence of cAMP. The results of our calculations are fully consistent with the available experimental data and suggest that the key factor of the cAMP allosteric mechanism in cNBDS's is the increased flexibility of the protein upon ligand release along with a mechanical coupling between helical segments. In addition, our calculations provide a rationale for the experimentally observed cAMP selective binding to PKA.
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Affiliation(s)
- Sergio Pantano
- International School for Advanced Studies (ISAS) and INFM - DEMOCRITOS Modeling Center for Research in Atomistic Simulation, Trieste, Italy.
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44
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Lynn GW, Heller WT, Mayasundari A, Minor KH, Peterson CB. A Model for the Three-Dimensional Structure of Human Plasma Vitronectin from Small-Angle Scattering Measurements. Biochemistry 2004; 44:565-74. [PMID: 15641781 DOI: 10.1021/bi048347s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small-angle X-ray scattering (SAXS) measurements were used to characterize vitronectin, a circulatory protein found in human plasma that functions in regulating cell adhesion and migration, as well as proteolytic cascades that affect blood coagulation, fibrinolysis, and pericellular proteolysis. SAXS measurements were taken over a 3-fold range of protein concentrations, yielding data that characterize a monodisperse system of particles with an average radius of gyration of 30.3 +/- 0.6 A and a maximum linear dimension of 110 A. Shape restoration was applied to the data to produce two models of the solution structure of the ligand-free protein. A low-resolution model of the protein was generated that indicates the protein to be roughly peanut-shaped. A better understanding of the domain structure of vitronectin resulted from low-resolution models developed from available high-resolution structures of the domains. These domains include the N-terminal domain that was determined experimentally by NMR [Mayasundari, A., Whittemore, N. A., Serpersu, E. H., and Peterson, C. B. (2004) J. Biol. Chem. 279, 29359-29366] and the docked structure of the central and C-terminal domains that were determined by computational threading [Xu, D., Baburaj, K., Peterson, C. B., and Xu, Y. (2001) Proteins: Struct., Funct., Genet. 44, 312-320]. This model provides an indication of the disposition of the central domain and C-terminal heparin-binding domains of vitronectin with respect to the N-terminal somatomedin B (SMB) domain. This model constructed from the available domain structures, which agrees with the low-resolution model produced from the SAXS data, shows the SMB domain well separated from the central and heparin-binding domains by a disordered linker (residues 54-130). Also, binding sites within the SMB domain are predicted to be well exposed to the surrounding solvent for ease of access to its various ligands.
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Affiliation(s)
- Gary W Lynn
- Center for Structural Molecular Biology and Condensed Matter Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Hamuro Y, Anand GS, Kim JS, Juliano C, Stranz DD, Taylor SS, Woods VL. Mapping intersubunit interactions of the regulatory subunit (RIalpha) in the type I holoenzyme of protein kinase A by amide hydrogen/deuterium exchange mass spectrometry (DXMS). J Mol Biol 2004; 340:1185-96. [PMID: 15236976 DOI: 10.1016/j.jmb.2004.05.042] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 05/13/2004] [Indexed: 11/24/2022]
Abstract
Protein kinase A (PKA), a central locus for cAMP signaling in the cell, is composed of regulatory (R) and catalytic (C) subunits. The C-subunits are maintained in an inactive state by binding to the R-subunit dimer in a tetrameric holoenzyme complex (R(2)C(2)). PKA is activated by cAMP binding to the R-subunits which induces a conformational change leading to release of the active C-subunit. Enzymatic activity of the C-subunit is thus regulated by cAMP via the R-subunit, which toggles between cAMP and C-subunit bound states. The R-subunit is composed of a dimerization/docking (D/D) domain connected to two cAMP-binding domains (cAMP:A and cAMP:B). While crystal structures of the free C-subunit and cAMP-bound states of a deletion mutant of the R-subunit are known, there is no structure of the holoenzyme complex or of the cAMP-free state of the R-subunit. An important step in understanding the cAMP-dependent activation of PKA is to map the R-C interface and characterize the mutually exclusive interactions of the R-subunit with cAMP and C-subunit. Amide hydrogen/deuterium exchange mass spectrometry is a suitable method that has provided insights into the different states of the R-subunit in solution, thereby allowing mapping of the effects of cAMP and C-subunit on different regions of the R-subunit. Our study has localized interactions with the C-subunit to a small contiguous surface on the cAMP:A domain and the linker region. In addition, C-subunit binding causes increased amide hydrogen exchange within both cAMP-domains, suggesting that these regions become more flexible in the holoenzyme and are primed to bind cAMP. Furthermore, the difference in the protection patterns between RIalpha and the previously studied RIIbeta upon cAMP-binding suggests isoform-specific differences in cAMP-dependent regulation of PKA activity.
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Affiliation(s)
- Yoshimoto Hamuro
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0656, USA
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Heller WT, Vigil D, Brown S, Blumenthal DK, Taylor SS, Trewhella J. C subunits binding to the protein kinase A RI alpha dimer induce a large conformational change. J Biol Chem 2004; 279:19084-90. [PMID: 14985329 DOI: 10.1074/jbc.m313405200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present structural data on the RI alpha isoform of the cAMP-dependent protein kinase A that reveal, for the first time, a large scale conformational change within the RI alpha homodimer upon catalytic subunit binding. This result infers that the inhibition of catalytic subunit activity is not the result of a simple docking process but rather is a multi-step process involving local conformational changes both in the cAMP-binding domains as well as in the linker region of the regulatory subunit that impact the global structure of the regulatory homodimer. The results were obtained using small-angle neutron scattering with contrast variation and deuterium labeling. From these experiments we derived information on the shapes and dispositions of the catalytic subunits and regulatory homodimer within a holoenzyme reconstituted with a deuterated regulatory subunit. The scattering data also show that, despite extensive sequence homology between the isoforms, the overall structure of the type I alpha holoenzyme is significantly more compact than the type II alpha isoform. We present a model of the type I alpha holoenzyme, built using available high-resolution structures of the component subunits and domains, which best fits the neutron-scattering data. In this model, the type I alpha holoenzyme forms a flattened V shape with the RI alpha dimerization domain at the point of the V and the cAMP-binding domains of the RI alpha subunits with their bound catalytic subunits at the ends.
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Affiliation(s)
- William T Heller
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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