Classification and Phylogenetic Analysis of the cAMP-Dependent Protein Kinase Regulatory Subunit Family

Cánaves, Jaume M.; Taylor, Susan S.

doi:10.1007/s00239-001-0013-1

Cited by 105 publications

(108 citation statements)

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“…Results Sequence Structure Analysis. As shown previously (1,4,12), sequences of CNB-containing domains found in many organisms are well aligned. Structural analyses confirmed that secondary structure assignments are also very similar to what is seen in Fig.…”

Section: Methodssupporting

confidence: 72%

“…1 b and c) where glutamic acid and arginine residues form specific hydrogen bonds with the O2Ј of the sugar and the O1P of the phosphate (1,12). These hydrogen bonds anchor the cAMP in a hydrophobic environment.…”

Section: Discussionmentioning

confidence: 99%

“…Although the best-known bacterial CNB domain is associated with the catabolite activator protein (CAP), is linked to a DNA binding domain, and mediates gene transcription in the absence of glucose, the elucidation of many bacterial genomes indicates that this module is much more diverse. There are literally hundreds of proteins that are linked to CNB domains, and these proteins mediate many types of stress responses (1).…”

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confidence: 99%

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The cAMP binding domain: An ancient signaling module

Berman

Eyck

Goodsell

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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195

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cAMP-binding domains from several different proteins were analyzed to determine the properties and interactions of this recognition motif. Systematic computational analyses, including structure-based sequence comparison, surface matching, affinity grid analysis, and analyses of the ligand protein interactions were carried out. These analyses show distinctive roles of the sugar phosphate and the adenine in the cAMP-binding module. We propose that the cAMPbinding regulatory proteins function by providing an allosteric system in which the presence or absence of cAMP produces a substantial structural change through the loss of hydrophobic interactions with the adenine ring and consequent repositioning of the C helix. The modified positioning of the helix in turn is recognized by a proteinbinding event, completing the allostery.allostery ͉ conserved cyclic nucleotide-binding motif C yclic AMP (cAMP) (Fig. 1a) is an ancient signaling molecule that serves as an indicator of stress from the most primitive bacteria to humans. The module that binds cAMP and translates the signal into a biological response, the cyclic nucleotidebinding (CNB) domain, is also ancient. Although the best-known bacterial CNB domain is associated with the catabolite activator protein (CAP), is linked to a DNA binding domain, and mediates gene transcription in the absence of glucose, the elucidation of many bacterial genomes indicates that this module is much more diverse. There are literally hundreds of proteins that are linked to CNB domains, and these proteins mediate many types of stress responses (1).The CNB domain is a small module, typically Ϸ120 aa, comprised of both ␤ strands and helical elements. The general organization of secondary structure of the essential cAMPbinding site is an eight-stranded ␤ barrel that functions as a basket. The cyclic nucleotide phosphate lies at the base of the ␤ barrel where it is well shielded from solvent and protected from phosphodiesterases (2). The most conserved feature of the ␤ barrel is the phosphate binding cassette (PBC) comprised of ␤ strand 6, a short turn of helix, and ␤ strand 7. A conserved feature of this PBC is a buried arginine that binds to the exocyclic phosphate of cAMP and a glutamate that binds the ribose 2Ј-OH. In addition to the ␤ barrel, the CNB module has a helical subdomain. The A helix precedes the ␤ barrel and is in an antiparallel manner with the B helix that immediately follows ␤ strand 8. The most variable feature of the domain is the C helix ( Fig. 1 b and c).The structure of the CNB domain was first revealed when the structure of CAP was determined (3). Based on sequence similarities, it was predicted that the fold would be conserved in the CNB domains associated with mammalian protein kinases (4), protein kinase A (PKA) and cGMP-dependent protein kinase (5). This prediction was confirmed when the structure of a deletion mutant of the RI␣ subunit of PKA was determined (6). RI␣ has two tandem CNB domains, each with a fold that resembles the CNB domain of CAP. The subsequent ...

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Section: Methodssupporting

confidence: 72%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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The cAMP binding domain: An ancient signaling module

Berman

Eyck

Goodsell

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

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213

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“…As organismal complexity increases, so theoretically does the requirement for an increased complement of signal transduction machinery. Whereas expansion of some kinase families appears to parallel increasing organismal complexity (1), the protein kinase A family has undergone little expansion (2) despite the large number of its physiological substrates distributed throughout the cell. Thus, intrinsic differences between protein kinase A family members cannot fully account for such diversity because, on their own, they do not provide sufficient specificity.…”

mentioning

confidence: 99%

Cross-species Sequence Analysis Reveals Multiple Charged Residue-rich Domains That Regulate Nuclear/Cytoplasmic Partitioning and Membrane Localization of A Kinase Anchoring Protein 12 (SSeCKS/Gravin)

Streb¹,

Miano

2005

Journal of Biological Chemistry

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A kinase anchoring proteins (AKAPs) assemble and compartmentalize multiprotein signaling complexes at discrete subcellular locales and thus confer specificity to transduction cascades using ubiquitous signaling enzymes, such as protein kinase A. Intrinsic targeting domains in each AKAP determine the subcellular localization of these complexes and, along with protein-protein interaction domains, form the core of AKAP function. As a foundational step toward elucidating the relationship between location and function, we have used cross-species sequence analysis and deletion mapping to facilitate the identification of the targeting determinants of AKAP12 (also known as SSeCKS or Gravin). Three charged residue-rich regions were identified that regulate two aspects of AKAP12 localization, nuclear/cytoplasmic partitioning and perinuclear/cell periphery targeting. Using deletion mapping and green fluorescent protein chimeras, we uncovered a heretofore unrecognized nuclear localization potential. Five nuclear localization signals, including a novel class of this type of signal termed X2-NLS, are found in the central region of AKAP12 and are important for nuclear targeting. However, this nuclear localization is suppressed by the negatively charged C terminus that mediates nuclear exclusion. In this condition, the distribution of AKAP12 is regulated by an N-terminal targeting domain that simultaneously directs perinuclear and peripheral AKAP12 localization. Three basic residue-rich regions in the Nterminal targeting region have similarity to the MARCKS proteins and were found to control AKAP12 localization to ganglioside-rich regions at the cell periphery. Our data suggest that AKAP12 localization is regulated by a hierarchy of targeting domains and that the localization of AKAP12-assembled signaling complexes may be dynamically regulated.Multicellular organisms require extensive signaling networks to coordinate physiological responses to a diverse array of stimuli. As organismal complexity increases, so theoretically does the requirement for an increased complement of signal transduction machinery. Whereas expansion of some kinase families appears to parallel increasing organismal complexity (1), the protein kinase A family has undergone little expansion (2) despite the large number of its physiological substrates distributed throughout the cell. Thus, intrinsic differences between protein kinase A family members cannot fully account for such diversity because, on their own, they do not provide sufficient specificity. Instead, specificity appears to be conferred by an ever expanding pseudo-family of anchoring proteins, the A kinase anchoring proteins (AKAPs), 1 that compartmentalize protein kinase A-containing signaling complexes to discrete subcellular locales (3).The intrinsic targeting and protein-protein interaction domains of each AKAP direct correct spatial and temporal assembly of protein kinase A-containing signaling complexes. Such compartmentalization simultaneously shields neighboring complexes from activated s...

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“…Mutagenesis (7) and hydrogen/deuterium exchange experiments (8) have identified the helical subdomain in the more N-terminal cAMP-binding domain (domain A) of RI␣ as an additional region of contact between the R and C subunits. There is high sequence homology between the isoforms in the D/D domain and the cAMPbinding domains, but the linker regions are quite different in length and sequence (9).…”

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confidence: 99%

C Subunits Binding to the Protein Kinase A RIα Dimer Induce a Large Conformational Change

Heller

Vigil

Brown

et al. 2004

Journal of Biological Chemistry

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We present structural data on the RI␣ isoform of the cAMP-dependent protein kinase A that reveal, for the first time, a large scale conformational change within the RI␣ 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␣ holoenzyme is significantly more compact than the type II␣ isoform. We present a model of the type I␣ 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␣ holoenzyme forms a flattened V shape with the RI␣ dimerization domain at the point of the V and the cAMP-binding domains of the RI␣ subunits with their bound catalytic subunits at the ends.Many cellular signaling pathways in eukaryotes involve protein kinases, which phosphorylate Ser, Thr, and Tyr residues in a variety of target proteins. The cAMP-dependent protein kinase A (PKA 1 or protein kinase A) is one of the best-studied members of the Ser/Thr protein kinase family. PKA is known to be involved in the regulation of a large number of cellular processes including metabolism, contractile activity, growth, apoptosis, and ion flux (1). Mutations in PKA can lead to diseases such as Carney complex (2) and lupus (3). The catalytic (C) subunits of PKA are responsible for catalyzing the phospho-transfer reaction, whereas the regulatory (R) subunits serve both to confer cAMP dependence and to localize the holoenzyme to discrete subcellular locations via interactions with A-kinase anchoring proteins (AKAPs) (4). At low cAMP concentrations, PKA is maintained as an inactive tetrameric holoenzyme complex (R 2 C 2 ) consisting of a homodimeric R 2 subunit and two C subunits. When intracellular concentrations of cAMP increase in response to specific cellular stimuli, four cAMP molecules bind to each R 2 subunit. This event causes a release of inhibition of C by R, allowing the C subunits to phosphorylate their target proteins.There are four major isoforms of PKA, types I␣, I␤, II␣, and II␤, which differ with respect to their R subunits (RI␣, RI␤, RII␣, and RII␤, respectively). The isoforms have different biological functions, as determined by genetic studies using mice. For instance, mice lacking the RI␣ gene die in utero (5), whereas mice lacking the RII␤ gene are viable, lean,...

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Classification and Phylogenetic Analysis of the cAMP-Dependent Protein Kinase Regulatory Subunit Family

Cited by 105 publications

References 52 publications

The cAMP binding domain: An ancient signaling module

The cAMP binding domain: An ancient signaling module

Cross-species Sequence Analysis Reveals Multiple Charged Residue-rich Domains That Regulate Nuclear/Cytoplasmic Partitioning and Membrane Localization of A Kinase Anchoring Protein 12 (SSeCKS/Gravin)

C Subunits Binding to the Protein Kinase A RIα Dimer Induce a Large Conformational Change

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