Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases

Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.

Download Full-text

Methods for Identification of Substrates/Inhibitors of FCP/SCP Type Protein Ser/Thr Phosphatases

Processes ◽

10.3390/pr8121598 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1598

Author(s):

Masataka Mizunuma ◽

Atsushi Kaneko ◽

Shunta Imai ◽

Kazuhiro Furukawa ◽

Yoshiro Chuman

Keyword(s):

Protein Phosphorylation ◽

Protein Kinases ◽

Substrate Recognition ◽

Phage Library ◽

Biological Functions ◽

Post Translational Modification ◽

Rigid Substrate ◽

Individual Protein ◽

Terminal Domain ◽

The Individual

Protein phosphorylation is the most widespread type of post-translational modification and is properly controlled by protein kinases and phosphatases. Regarding the phosphorylation of serine (Ser) and threonine (Thr) residues, relatively few protein Ser/Thr phosphatases control the specific dephosphorylation of numerous substrates, in contrast with Ser/Thr kinases. Recently, protein Ser/Thr phosphatases were reported to have rigid substrate recognition and exert various biological functions. Therefore, identification of targeted proteins by individual protein Ser/Thr phosphatases is crucial to clarify their own biological functions. However, to date, information on the development of methods for identification of the substrates of protein Ser/Thr phosphatases remains scarce. In turn, substrate-trapping mutants are powerful tools to search the individual substrates of protein tyrosine (Tyr) phosphatases. This review focuses on the development of novel methods for the identification of Ser/Thr phosphatases, especially small C-terminal domain phosphatase 1 (Scp1), using peptide-displayed phage library with AlF4−/BeF3−, and discusses the identification of putative inhibitors.

Download Full-text

Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry

Biochemical Journal ◽

10.1042/bj20021547 ◽

2003 ◽

Vol 370 (2) ◽

pp. 373-389 ◽

Cited By ~ 74

Author(s):

Peter J. KENNELLY

Keyword(s):

Protein Phosphorylation ◽

Protein Kinases ◽

Regulatory Mechanism ◽

Protein Phosphatases ◽

Critical Role ◽

Bacterial Protein ◽

Archaeal Protein ◽

Recent Addition ◽

Multicellular Organisms ◽

The Impact

Protein phosphorylation/dephosphorylation has long been considered a recent addition to Nature's regulatory arsenal. Early studies indicated that this molecular regulatory mechanism existed only in higher eukaryotes, suggesting that protein phosphorylation/dephosphorylation had emerged to meet the particular signal-transduction requirements of multicellular organisms. Although it has since become apparent that simple eukaryotes and even bacteria are sites of protein phosphorylation/dephosphorylation, the perception widely persists that this molecular regulatory mechanism emerged late in evolution, i.e. after the divergence of the contemporary phylogenetic domains. Only highly developed cells, it was reasoned, could afford the high ‘overhead’ costs inherent in the acquisition of dedicated protein kinases and protein phosphatases. The advent of genome sequencing has provided an opportunity to exploit Nature's phylogenetic diversity as a vehicle for critically examining this hypothesis. In tracing the origins and evolution of protein phosphorylation/dephosphorylation, the members of the Archaea, the so-called ‘third domain of life’, will play a critical role. Whereas several studies have demonstrated that archaeal proteins are subject to modification by covalent phosphorylation, relatively little is known concerning the identities of the proteins affected, the impact on their functional properties, or the enzymes that catalyse these events. However, examination of several archaeal genomes has revealed the widespread presence of several ostensibly ‘eukaryotic’ and ‘bacterial’ protein kinase and protein phosphatase paradigms. Similar findings of ‘phylogenetic trespass’ in members of the Eucarya (eukaryotes) and the Bacteria suggest that this versatile molecular regulatory mechanism emerged at an unexpectedly early point in development of ‘life as we know it'.

Download Full-text

PP2A Phosphatases Take a Giant Leap in the Post-Genomics Era

Current Genomics ◽

10.2174/1389202920666190517110605 ◽

2019 ◽

Vol 20 (3) ◽

pp. 154-171

Author(s):

Malathi Bheri ◽

Girdhar K. Pandey

Keyword(s):

Functional Genomics ◽

Protein Phosphorylation ◽

Growth And Development ◽

Signaling Cascades ◽

Post Translational Modification ◽

Cellular Processes ◽

Regulatory Processes ◽

Giant Leap ◽

Signaling Components ◽

Functional Versatility

Background: Protein phosphorylation is an important reversible post-translational modification, which regulates a number of critical cellular processes. Phosphatases and kinases work in a concerted manner to act as a “molecular switch” that turns-on or - off the regulatory processes driving the growth and development under normal circumstances, as well as responses to multiple stresses in plant system. The era of functional genomics has ushered huge amounts of information to the framework of plant systems. The comprehension of who’s who in the signaling pathways is becoming clearer and the investigations challenging the conventional functions of signaling components are on a rise. Protein phosphatases have emerged as key regulators in the signaling cascades. PP2A phosphatases due to their diverse holoenzyme compositions are difficult to comprehend. Conclusion: In this review, we highlight the functional versatility of PP2A members, deciphered through the advances in the post-genomic era.

Download Full-text

Review Lecture: Protein phosphorylation and hormone action

Proceedings of the Royal Society of London Series B Biological Sciences ◽

10.1098/rspb.1988.0040 ◽

1988 ◽

Vol 234 (1275) ◽

pp. 115-144 ◽

Cited By ~ 146

Keyword(s):

Protein Kinases ◽

Conformational Changes ◽

Protein Phosphatases ◽

Second Messengers ◽

Cellular Processes ◽

Extracellular Signals ◽

Steady State Levels ◽

Pleiotropic Actions ◽

Signalling Systems ◽

Chemical Mediators

Many key regulatory proteins exist in cells as either a phosphorylated or a dephosphorylated form, their steady-state levels of phosphorylation reflecting the relative activities of the protein kinases and protein phosphatases that catalyse the interconversion process. Phosphorylation of seryl or threonyl (and occasionally tyrosyl) residues triggers small conformational changes in these proteins that alter their biological properties. Hormones and other extracellular signals transmit information to the interior of the cell by activating transmembrane signalling systems that control the production of a relatively small number of chemical mediators, termed ‘second messengers’. These substances regulate the activities of protein kinases and phosphatases, and so alter the phosphorylation states of many intracellular proteins, accounting for the diversity of action of hormones. In this lecture I review recent work which demonstrates that a wide variety of cellular processes are controlled by relatively few protein kinases and protein phosphatases with pleiotropic actions. These enzymes provide the basis of an interlocking network that allows extracellular signals to coordinate biochemical functions.

Download Full-text

Progesterone receptors act as sensors for mitogenic protein kinases in breast cancer models

Endocrine Related Cancer ◽

10.1677/erc-08-0281 ◽

2009 ◽

Vol 16 (2) ◽

pp. 351-361 ◽

Cited By ~ 33

Author(s):

Gwen E Dressing ◽

Christy R Hagan ◽

Todd P Knutson ◽

Andrea R Daniel ◽

Carol A Lange

Keyword(s):

Breast Cancer ◽

Protein Kinases ◽

Cell Cycle Progression ◽

Progesterone Receptors ◽

Cancer Cell Line ◽

Mitogen Activated Protein Kinase ◽

Post Translational Modification ◽

Cellular Processes ◽

Mitogen Activated Protein ◽

Regulatory Input

Progesterone receptors (PR), members of the nuclear receptor superfamily, function as ligand-activated transcription factors and initiators of c-Src kinase and mitogen-activated protein kinase signaling. Bidirectional cross-talk between PR and mitogenic protein kinases results in changes in PR post-translational modification, leading to alterations in PR transcriptional activity and promoter selectivity. PR-induced rapid activation of cytoplasmic protein kinases insures precise regulatory input to downstream cellular processes that are dependent upon nuclear PR, such as cell-cycle progression, and pro-survival signaling. Here, we review interactions between PR and mitogenic protein kinases and discuss the consequences of specific post-translational modifications on PR action in breast cancer cell-line models.

Download Full-text

Recent developments in mass spectrometry-based quantitative phosphoproteomicsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

Biochemistry and Cell Biology ◽

10.1139/o08-007 ◽

2008 ◽

Vol 86 (2) ◽

pp. 137-148 ◽

Cited By ~ 27

Author(s):

Jeffrey C. Smith ◽

Daniel Figeys

Keyword(s):

Mass Spectrometry ◽

Protein Phosphorylation ◽

Review Process ◽

Peer Review Process ◽

Cellular Systems ◽

Post Translational Modification ◽

Dynamic Nature ◽

Cellular Processes ◽

Recent Developments ◽

Selection Of

Protein phosphorylation is a reversible post-translational modification that is involved in virtually all eukaryotic cellular processes and has been studied in great detail in recent years. Many developments in mass spectrometry (MS)-based proteomics have been successfully applied to study protein phosphorylation in highly complicated samples. Furthermore, the emergence of a variety of enrichment strategies has allowed some of the challenges associated with low phosphorylation stoichiometry and phosphopeptide copy number to be overcome. The dynamic nature of protein phosphorylation complicates its analysis; however, a number of methods have been developed to successfully quantitate phosphorylation changes in a variety of cellular systems. The following review details some of the most recent breakthroughs in the study of protein phosphorylation, or phosphoproteomics, using MS-based approaches. The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics.

Download Full-text

The regulation of protein phosphorylation

Biochemical Society Transactions ◽

10.1042/bst0370627 ◽

2009 ◽

Vol 37 (4) ◽

pp. 627-641 ◽

Cited By ~ 169

Author(s):

Louise N. Johnson

Keyword(s):

Protein Phosphorylation ◽

Protein Kinases ◽

Drug Targets ◽

Cell Cycle Progression ◽

Catalytic Domain ◽

Cell Movement ◽

Cellular Processes ◽

Cell Life ◽

Diseased State ◽

And Control

Phosphorylation plays essential roles in nearly every aspect of cell life. Protein kinases regulate signalling pathways and cellular processes that mediate metabolism, transcription, cell-cycle progression, differentiation, cytoskeleton arrangement and cell movement, apoptosis, intercellular communication, and neuronal and immunological functions. Protein kinases share a conserved catalytic domain, which catalyses the transfer of the γ-phosphate of ATP to a serine, threonine or tyrosine residue in protein substrates. The kinase can exist in an active or inactive state regulated by a variety of mechanisms in different kinases that include control by phosphorylation, regulation by additional domains that may target other molecules, binding and regulation by additional subunits, and control by protein–protein association. This Novartis Medal Lecture was delivered at a meeting on protein evolution celebrating the 200th anniversary of Charles Darwin's birth. I begin with a summary of current observations from protein sequences of kinase phylogeny. I then review the structural consequences of protein phosphorylation using our work on glycogen phosphorylase to illustrate one of the more dramatic consequences of phosphorylation. Regulation of protein phosphorylation is frequently disrupted in the diseased state, and protein kinases have become high-profile targets for drug development. Finally, I consider recent advances on protein kinases as drug targets and describe some of our recent work with CDK9 (cyclin-dependent kinase 9)–cyclin T, a regulator of transcription.

Download Full-text