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Andresen H, Pérez‐Ternero C, Robinson J, Dickey DM, Hobbs AJ, Potter LR, Levy FO, Cataliotti A, Moltzau LR. Novel enhancers of guanylyl cyclase-A activity acting via allosteric modulation. Br J Pharmacol 2023; 180:3254-3270. [PMID: 37522273 PMCID: PMC10952227 DOI: 10.1111/bph.16203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND AND PURPOSE Guanylyl cyclase-A (GC-A), activated by endogenous atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), plays an important role in the regulation of cardiovascular and renal homeostasis and is an attractive drug target. Even though small molecule modulators allow oral administration and longer half-life, drug targeting of GC-A has so far been limited to peptides. Thus, in this study we aimed to develop small molecular activators of GC-A. EXPERIMENTAL APPROACH Hits were identified through high-throughput screening and optimized by in silico design. Cyclic GMP was measured in QBIHEK293A cells expressing GC-A, GC-B or chimerae of the two receptors using AlphaScreen technology. Binding assays were performed in membrane preparations or whole cells using 125 I-ANP. Vasorelaxation was measured in aortic rings isolated from Wistar rats. KEY RESULTS We have identified small molecular allosteric enhancers of GC-A, which enhanced ANP or BNP effects in cellular systems and ANP-induced vasorelaxation in rat aortic rings. The mechanism of action appears novel and not mediated through previously described allosteric binding sites. In addition, the selectivity and activity depend on a single amino acid residue that differs between the two similar receptors GC-A and GC-B. CONCLUSION AND IMPLICATIONS We describe a novel allosteric binding site on GC-A, which can be targeted by small molecules to enhance ANP and BNP effects. These compounds will be valuable tools in further development and proof-of-concept of GC-A enhancement for the potential use in cardiovascular therapy.
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Affiliation(s)
- Henriette Andresen
- Department of Pharmacology, Institute of Clinical MedicineUniversity of Oslo and Oslo University HospitalOsloNorway
- Institute for Experimental Medical ResearchUniversity of Oslo and Oslo University HospitalOsloNorway
| | - Cristina Pérez‐Ternero
- William Harvey Research Institute, Barts & The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Jerid Robinson
- Department of Biochemistry, Molecular Biology, and BiophysicsUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Deborah M. Dickey
- Department of Biochemistry, Molecular Biology, and BiophysicsUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Adrian J. Hobbs
- William Harvey Research Institute, Barts & The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Lincoln R. Potter
- Department of Biochemistry, Molecular Biology, and BiophysicsUniversity of Minnesota Medical SchoolMinneapolisMinnesotaUSA
| | - Finn Olav Levy
- Department of Pharmacology, Institute of Clinical MedicineUniversity of Oslo and Oslo University HospitalOsloNorway
| | - Alessandro Cataliotti
- Institute for Experimental Medical ResearchUniversity of Oslo and Oslo University HospitalOsloNorway
| | - Lise Román Moltzau
- Department of Pharmacology, Institute of Clinical MedicineUniversity of Oslo and Oslo University HospitalOsloNorway
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2
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Otto NM, Potter LR. Vicinal glutamates are better phosphomimetics: Phosphorylation is required for allosteric activation of guanylyl cyclase-A. Front Mol Neurosci 2022; 15:1012784. [DOI: 10.3389/fnmol.2022.1012784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
Multisite phosphorylation of guanylyl cyclase (GC)-A, also known as NPR-A or NPR1, is required for receptor activation by natriuretic peptides (NPs) because alanine substitutions for the first four GC-A phosphorylation sites produce an enzyme that cannot be stimulated by NPs. In contrast, single Glu substitutions for the first six chemically identified GC-A phosphorylation sites to mimic the negative charge of phosphate produced an enzyme that is activated by NPs but had an elevated Michaelis constant (Km), resulting in low activity. Here, we show that vicinal (double adjacent) Glu substitutions for the same sites to mimic the two negative charges of phosphate produced a near wild type (WT) enzyme with a low Km. Unlike the enzyme with single glutamate substitutions, the vicinally substituted enzyme did not require the functionally identified Ser-473-Glu substitution to achieve WT-like activity. Importantly, the negative charge associated with either phosphorylation or glutamate substitutions was required for allosteric activation of GC-A by ATP. We conclude that vicinal Glu substitutions are better phosphomimetics than single Glu substitutions and that phosphorylation is required for allosteric activation of GC-A in the absence and presence of NP. Finally, we suggest that the putative functionally identified phosphorylation sites, Ser-473 in GC-A and Ser-489 in GC-B, are not phosphorylation sites at all.
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3
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Egbert JR, Uliasz TF, Lowther KM, Kaback D, Wagner BM, Healy CL, O’Connell TD, Potter LR, Jaffe LA, Yee SP. Epitope-tagged and phosphomimetic mouse models for investigating natriuretic peptide-stimulated receptor guanylyl cyclases. Front Mol Neurosci 2022; 15:1007026. [PMID: 36340689 PMCID: PMC9627482 DOI: 10.3389/fnmol.2022.1007026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/28/2022] [Indexed: 01/25/2023] Open
Abstract
The natriuretic peptide receptors NPR1 and NPR2, also known as guanylyl cyclase A and guanylyl cyclase B, have critical functions in many signaling pathways, but much remains unknown about their localization and function in vivo. To facilitate studies of these proteins, we developed genetically modified mouse lines in which endogenous NPR1 and NPR2 were tagged with the HA epitope. To investigate the role of phosphorylation in regulating NPR1 and NPR2 guanylyl cyclase activity, we developed mouse lines in which regulatory serines and threonines were substituted with glutamates, to mimic the negative charge of the phosphorylated forms (NPR1-8E and NPR2-7E). Here we describe the generation and applications of these mice. We show that the HA-NPR1 and HA-NPR2 mice can be used to characterize the relative expression levels of these proteins in different tissues. We describe studies using the NPR2-7E mice that indicate that dephosphorylation of NPR2 transduces signaling pathways in ovary and bone, and studies using the NPR1-8E mice that indicate that the phosphorylation state of NPR1 is a regulator of heart, testis, and adrenal function.
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Affiliation(s)
- Jeremy R. Egbert
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States,*Correspondence: Jeremy R. Egbert,
| | - Tracy F. Uliasz
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States
| | - Katie M. Lowther
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States,Center for Mouse Genome Modification, University of Connecticut Health Center, Farmington, CT, United States
| | - Deborah Kaback
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States,Center for Mouse Genome Modification, University of Connecticut Health Center, Farmington, CT, United States
| | - Brandon M. Wagner
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, United States
| | - Chastity L. Healy
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, United States
| | - Timothy D. O’Connell
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, United States
| | - Lincoln R. Potter
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, United States,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, United States,Lincoln R. Potter,
| | - Laurinda A. Jaffe
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States,Laurinda A. Jaffe,
| | - Siu-Pok Yee
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, United States,Center for Mouse Genome Modification, University of Connecticut Health Center, Farmington, CT, United States,Siu-Pok Yee,
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4
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Sheetz JB, Lemmon MA. Looking lively: emerging principles of pseudokinase signaling. Trends Biochem Sci 2022; 47:875-891. [PMID: 35585008 PMCID: PMC9464697 DOI: 10.1016/j.tibs.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
Progress towards understanding catalytically 'dead' protein kinases - pseudokinases - in biology and disease has hastened over the past decade. An especially lively area for structural biology, pseudokinases appear to be strikingly similar to their kinase relatives, despite lacking key catalytic residues. Distinct active- and inactive-like conformation states, which are crucial for regulating bona fide protein kinases, are conserved in pseudokinases and appear to be essential for function. We discuss recent structural data on conformational transitions and nucleotide binding by pseudokinases, from which some common principles emerge. In both pseudokinases and bona fide kinases, a conformational toggle appears to control the ability to interact with signaling effectors. We also discuss how biasing this conformational toggle may provide opportunities to target pseudokinases pharmacologically in disease.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
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5
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Purification, characterization, and preliminary serial crystallography diffraction advances structure determination of full-length human particulate guanylyl cyclase A receptor. Sci Rep 2022; 12:11824. [PMID: 35821229 PMCID: PMC9276669 DOI: 10.1038/s41598-022-15798-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Particulate Guanylyl Cyclase Receptor A (pGC-A) is a natriuretic peptide membrane receptor, playing a vital role in controlling cardiovascular, renal, and endocrine functions. The extracellular domain interacts with natriuretic peptides and triggers the intracellular guanylyl cyclase domain to convert GTP to cGMP. To effectively develop methods to regulate pGC-A, structural information on the full-length form is needed. However, structural data on the transmembrane and intracellular domains are lacking. This work presents expression and optimization using baculovirus, along with the first purification of functional full-length human pGC-A. In vitro assays revealed the pGC-A tetramer was functional in detergent micelle solution. Based on our purification results and previous findings that dimer formation is required for functionality, we propose a tetramer complex model with two functional subunits. Previous research suggested pGC-A signal transduction is an ATP-dependent, two-step mechanism. Our results show the binding ligand also moderately activates pGC-A, and ATP is not crucial for activation of guanylyl cyclase. Furthermore, crystallization of full-length pGC-A was achieved, toward determination of its structure. Needle-shaped crystals with 3 Å diffraction were observed by serial crystallography. This work paves the road for determination of the full-length pGC-A structure and provides new information on the signal transduction mechanism.
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6
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Bose A, Visweswariah SS. The pseudokinase domain in receptor guanylyl cyclases. Methods Enzymol 2022; 667:535-574. [PMID: 35525553 DOI: 10.1016/bs.mie.2022.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cyclic GMP is produced by enzymes called guanylyl cyclases, of which the membrane-associated forms contain an intracellular pseudokinase domain that allosterically regulates the C-terminal guanylyl cyclase domain. Ligand binding to the extracellular domain of these single transmembrane-spanning domain receptors elicits an increase in cGMP levels in the cell. The pseudokinase domain (or kinase-homology domain) in these receptors appears to be critical for ligand-mediated activation. While the pseudokinase domain does not possess kinase activity, biochemical evidence indicates that the domain can bind ATP and thereby allosterically regulate the catalytic activity of these receptors. The pseudokinase domain also appears to be the site of interaction of regulatory proteins, as seen in the retinal guanylyl cyclases that are involved in visual signal transduction. In the absence of structural information on the pseudokinase-guanylyl cyclase domain organization of any member of this family of receptors, biochemical evidence has provided clues to the physical interaction of the pseudokinase and guanylyl cyclase domain. An α-helical linker region between the pseudokinase domain and the guanylyl cyclase domain regulates the basal activity of these receptors in the absence of a stimulatory ligand and is important for stabilizing the structure of the pseudokinase domain that can bind ATP. Here, we present an overview of salient features of ATP-mediated regulation of receptor guanylyl cyclases and describe biochemical approaches that allow a clearer understanding of the intricate interplay between the pseudokinase domain and catalytic domain in these proteins.
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Affiliation(s)
- Avipsa Bose
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India.
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7
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Wagner BM, Robinson JW, Healy CL, Gauthier M, Dickey DM, Yee SP, Osborn JW, O’Connell TD, Potter LR. Guanylyl cyclase-A phosphorylation decreases cardiac hypertrophy and improves systolic function in male, but not female, mice. FASEB J 2022; 36:e22069. [PMID: 34859913 PMCID: PMC8826535 DOI: 10.1096/fj.202100600rrr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023]
Abstract
Atrial natriuretic peptide (NP) and BNP increase cGMP, which reduces blood pressure and cardiac hypertrophy by activating guanylyl cyclase (GC)-A, also known as NPR-A or Npr1. Although GC-A is highly phosphorylated, and dephosphorylation inactivates the enzyme, the significance of GC-A phosphorylation to heart structure and function remains unknown. To identify in vivo processes that are regulated by GC-A phosphorylation, we substituted glutamates for known phosphorylation sites to make GC-A8E/8E mice that express an enzyme that cannot be inactivated by dephosphorylation. GC-A activity, but not protein, was increased in heart and kidney membranes from GC-A8E/8E mice. Activities were threefold higher in female compared to male cardiac ventricles. Plasma cGMP and testosterone were elevated in male and female GC-A8E/8E mice, but aldosterone was only increased in mutant male mice. Plasma and urinary creatinine concentrations were decreased and increased, respectively, but blood pressure and heart rate were unchanged in male GC-A8E/8E mice. Heart weight to body weight ratios for GC-A8E/8E male, but not female, mice were 12% lower with a 14% reduction in cardiomyocyte cross-sectional area. Subcutaneous injection of fsANP, a long-lived ANP analog, increased plasma cGMP and decreased aldosterone in male GC-AWT/WT and GC-A8E/8E mice at 15 min, but only GC-A8E/8E mice had elevated levels of plasma cGMP and aldosterone at 60 min. fsANP reduced ventricular ERK1/2 phosphorylation to a greater extent and for a longer time in the male mutant compared to WT mice. Finally, ejection fractions were increased in male but not female hearts from GC-A8E/8E mice. We conclude that increased phosphorylation-dependent GC-A activity decreases cardiac ERK activity, which results in smaller male hearts with improved systolic function.
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Affiliation(s)
- Brandon M. Wagner
- Department of Integrative Biology and Physiology, University of Minnesota, Medical School, Minneapolis, MN 55455 USA
| | - Jerid W. Robinson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Medical School, Minneapolis, MN 55455 USA
| | - Chastity L. Healy
- Department of Integrative Biology and Physiology, University of Minnesota, Medical School, Minneapolis, MN 55455 USA
| | - Madeline Gauthier
- Department of Integrative Biology and Physiology, University of Minnesota, Medical School, Minneapolis, MN 55455 USA
| | - Deborah M. Dickey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Medical School, Minneapolis, MN 55455 USA
| | - Siu-Pok Yee
- Department of Cell Biology at the University of Connecticut Health Center, Farmington, CT 06030 USA
| | - John W. Osborn
- Department of Surgery at the University of Minnesota, Medical School, Minneapolis, MN 55455 USA
| | - Timothy D. O’Connell
- Department of Integrative Biology and Physiology, University of Minnesota, Medical School, Minneapolis, MN 55455 USA,,Corresponding authors: Timothy D O’Connell , Lincoln R Potter
| | - Lincoln R. Potter
- Department of Integrative Biology and Physiology, University of Minnesota, Medical School, Minneapolis, MN 55455 USA,,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Medical School, Minneapolis, MN 55455 USA,,Corresponding authors: Timothy D O’Connell , Lincoln R Potter
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8
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Hofmann F. The cGMP system: components and function. Biol Chem 2021; 401:447-469. [PMID: 31747372 DOI: 10.1515/hsz-2019-0386] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 12/29/2022]
Abstract
The cyclic guanosine monophosphate (cGMP) signaling system is one of the most prominent regulators of a variety of physiological and pathophysiological processes in many mammalian and non-mammalian tissues. Targeting this pathway by increasing cGMP levels has been a very successful approach in pharmacology as shown for nitrates, phosphodiesterase (PDE) inhibitors and stimulators of nitric oxide-guanylyl cyclase (NO-GC) and particulate GC (pGC). This is an introductory review to the cGMP signaling system intended to introduce those readers to this system, who do not work in this area. This article does not intend an in-depth review of this system. Signal transduction by cGMP is controlled by the generating enzymes GCs, the degrading enzymes PDEs and the cGMP-regulated enzymes cyclic nucleotide-gated ion channels, cGMP-dependent protein kinases and cGMP-regulated PDEs. Part A gives a very concise introduction to the components. Part B gives a very concise introduction to the functions modulated by cGMP. The article cites many recent reviews for those who want a deeper insight.
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Affiliation(s)
- Franz Hofmann
- Pharmakologisches Institut, Technische Universität München, Biedersteiner Str. 29, D-80802 München, Germany
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9
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Bose A, Banerjee S, Visweswariah SS. Mutational landscape of receptor guanylyl cyclase C: Functional analysis and disease-related mutations. IUBMB Life 2020; 72:1145-1159. [PMID: 32293781 DOI: 10.1002/iub.2283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/18/2022]
Abstract
Guanylyl cyclase C (GC-C) is the receptor for the heat-stable enterotoxin, which causes diarrhea, and the endogenous ligands, guanylin and uroguanylin. GC-C is predominantly expressed in the intestinal epithelium and regulates fluid and ion secretion in the gut. The receptor has a complex domain organization, and in the absence of structural information, mutational analysis provides clues to mechanisms of regulation of this protein. Here, we review the mutational landscape of this receptor that reveals regulatory features critical for its activity. We also summarize the available information on mutations in GC-C that have been reported in humans and contribute to severe gastrointestinal abnormalities. Since GC-C is also expressed in extra-intestinal tissues, it is likely that mutations thus far reported in humans may also affect other organ systems, warranting a close observation of these patients in future.
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Affiliation(s)
- Avipsa Bose
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sanghita Banerjee
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sandhya S Visweswariah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
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10
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Zaru R, Magrane M, Orchard S. Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. FEBS J 2019; 287:4114-4127. [PMID: 31618524 DOI: 10.1111/febs.15100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 12/14/2022]
Abstract
The universal protein knowledgebase (UniProtKB) collects and centralises functional information on proteins across a wide range of species. In addition to the functional information added to all protein entries, for enzymes, which represent 20-40% of most proteomes, UniProtKB provides additional information about Enzyme Commission classification, catalytic activity, cofactors, enzyme regulation, kinetics and pathways, all based on critical assessment of published experimental data. Computer-based analysis and structural data are used to enrich the annotation of the sequence through the identification of active sites and binding sites. While the annotation of enzymes is well-defined, the curation of pseudoenzymes in UniProtKB has highlighted some challenges: how to identify them, how to assess their lack of catalytic activity, how to annotate their lack of catalytic activity in a consistent way and how much can be inferred and propagated from experimental data obtained from other species. Through various examples, we illustrate some of these issues and discuss some of the changes we propose to enhance the annotation and discovery of pseudoenzymes. Ultimately, improving the curation of pseudoenzymes will provide the scientific community with a comprehensive resource for pseudoenzymes, which in turn will lead to a better understanding of the evolution of these molecules, the aetiology of related diseases and the development of drugs.
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Affiliation(s)
- Rossana Zaru
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
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- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.,SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland.,Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA.,Protein Information Resource, University of Delaware, Newark, DE, USA
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11
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Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA. Emerging concepts in pseudoenzyme classification, evolution, and signaling. Sci Signal 2019; 12:eaat9797. [PMID: 31409758 DOI: 10.1126/scisignal.aat9797] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 21st century is witnessing an explosive surge in our understanding of pseudoenzyme-driven regulatory mechanisms in biology. Pseudoenzymes are proteins that have sequence homology with enzyme families but that are proven or predicted to lack enzyme activity due to mutations in otherwise conserved catalytic amino acids. The best-studied pseudoenzymes are pseudokinases, although examples from other families are emerging at a rapid rate as experimental approaches catch up with an avalanche of freely available informatics data. Kingdom-wide analysis in prokaryotes, archaea and eukaryotes reveals that between 5 and 10% of proteins that make up enzyme families are pseudoenzymes, with notable expansions and contractions seemingly associated with specific signaling niches. Pseudoenzymes can allosterically activate canonical enzymes, act as scaffolds to control assembly of signaling complexes and their localization, serve as molecular switches, or regulate signaling networks through substrate or enzyme sequestration. Molecular analysis of pseudoenzymes is rapidly advancing knowledge of how they perform noncatalytic functions and is enabling the discovery of unexpected, and previously unappreciated, functions of their intensively studied enzyme counterparts. Notably, upon further examination, some pseudoenzymes have previously unknown enzymatic activities that could not have been predicted a priori. Pseudoenzymes can be targeted and manipulated by small molecules and therefore represent new therapeutic targets (or anti-targets, where intervention should be avoided) in various diseases. In this review, which brings together broad bioinformatics and cell signaling approaches in the field, we highlight a selection of findings relevant to a contemporary understanding of pseudoenzyme-based biology.
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Affiliation(s)
- António J M Ribeiro
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sayoni Das
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Natalie Dawson
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Rossana Zaru
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sandra Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Christine Orengo
- Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, Molecular and Cellular Biology, Faculty of Biological Sciences, Astbury Building, Room 8.109, University of Leeds, Leeds LS2 9JT, UK
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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