Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4
Abstract
Phosphodiesterase 4 (PDE4) is an essential contributor to intracellular signaling and an important drug target. The four members of this enzyme family (PDE4A to -D) are functional dimers in which each subunit contains two upstream conserved regions (UCR), UCR1 and -2, which precede the C-terminal catalytic domain. Alternative promoters, transcriptional start sites, and mRNA splicing lead to the existence of over 25 variants of PDE4, broadly classified as long, short, and supershort forms. We report the X-ray crystal structure of long form PDE4B containing UCR1, UCR2, and the catalytic domain, crystallized as a dimer in which a disulfide bond cross-links cysteines engineered into UCR2 and the catalytic domain. Biochemical and mass spectrometric analyses showed that the UCR2-catalytic domain interaction occurs in trans, and established that this interaction regulates the catalytic activity of PDE4. By elucidating the key structural determinants of dimerization, we show that only long forms of PDE4 can be regulated by this mechanism. The results also provide a structural basis for the long-standing observation of high- and low-affinity binding sites for the prototypic inhibitor rolipram.
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- INDUSTRY
- OSTI Identifier:
- 1182326
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Volume: 112; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences, Washington, DC (United States)
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Cedervall, Peder, Aulabaugh, Ann, Geoghegan, Kieran F., McLellan, Thomas J., and Pandit, Jayvardhan. Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4. United States: N. p., 2015.
Web. doi:10.1073/pnas.1419906112.
Cedervall, Peder, Aulabaugh, Ann, Geoghegan, Kieran F., McLellan, Thomas J., & Pandit, Jayvardhan. Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4. United States. https://doi.org/10.1073/pnas.1419906112
Cedervall, Peder, Aulabaugh, Ann, Geoghegan, Kieran F., McLellan, Thomas J., and Pandit, Jayvardhan. Mon .
"Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4". United States. https://doi.org/10.1073/pnas.1419906112. https://www.osti.gov/servlets/purl/1182326.
@article{osti_1182326,
title = {Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4},
author = {Cedervall, Peder and Aulabaugh, Ann and Geoghegan, Kieran F. and McLellan, Thomas J. and Pandit, Jayvardhan},
abstractNote = {Phosphodiesterase 4 (PDE4) is an essential contributor to intracellular signaling and an important drug target. The four members of this enzyme family (PDE4A to -D) are functional dimers in which each subunit contains two upstream conserved regions (UCR), UCR1 and -2, which precede the C-terminal catalytic domain. Alternative promoters, transcriptional start sites, and mRNA splicing lead to the existence of over 25 variants of PDE4, broadly classified as long, short, and supershort forms. We report the X-ray crystal structure of long form PDE4B containing UCR1, UCR2, and the catalytic domain, crystallized as a dimer in which a disulfide bond cross-links cysteines engineered into UCR2 and the catalytic domain. Biochemical and mass spectrometric analyses showed that the UCR2-catalytic domain interaction occurs in trans, and established that this interaction regulates the catalytic activity of PDE4. By elucidating the key structural determinants of dimerization, we show that only long forms of PDE4 can be regulated by this mechanism. The results also provide a structural basis for the long-standing observation of high- and low-affinity binding sites for the prototypic inhibitor rolipram.},
doi = {10.1073/pnas.1419906112},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = ,
volume = 112,
place = {United States},
year = {Mon Mar 09 00:00:00 EDT 2015},
month = {Mon Mar 09 00:00:00 EDT 2015}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 48 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Human Recombinant Phosphodiesterase 4B2B Binds ( R )-Rolipram at a Single Site with Two Affinities
journal, November 1997
- Rocque, Warren J.; Tian, Gaochao; Wiseman, Jeffrey S.
- Biochemistry, Vol. 36, Issue 46
Comparison of Recombinant Human PDE4 Isoforms
journal, June 1998
- Saldou, Natalie; Obernolte, Rena; Huber, Anita
- Cellular Signalling, Vol. 10, Issue 6
A family of human phosphodiesterases homologous to the dunce learning and memory gene product of Drosophila melanogaster are potential targets for antidepressant drugs.
journal, October 1993
- Bolger, G.; Michaeli, T.; Martins, T.
- Molecular and Cellular Biology, Vol. 13, Issue 10
PRKAR1A and PDE4D Mutations Cause Acrodysostosis but Two Distinct Syndromes with or without GPCR-Signaling Hormone Resistance
journal, December 2012
- Linglart, Agnès; Fryssira, Helena; Hiort, Olaf
- The Journal of Clinical Endocrinology & Metabolism, Vol. 97, Issue 12
The MAP kinase ERK2 inhibits the cyclic AMP-specific phosphodiesterase HSPDE4D3 by phosphorylating it at Ser579
journal, February 1999
- Hoffmann, Ralf; Baillie, George S.; MacKenzie, Simon J.
- The EMBO Journal, Vol. 18, Issue 4
Phosphorylation and Activation of a cAMP-specific Phosphodiesterase by the cAMP-dependent Protein Kinase: INVOLVEMENT OF SERINE 54 IN THE ENZYME ACTIVATION
journal, July 1996
- Sette, Claudio; Conti, Marco
- Journal of Biological Chemistry, Vol. 271, Issue 28
Recombinant Expression of a Type IV, cAMP-Specific Phosphodiesterase: Characterization and Structure−Function Studies of Deletion Mutants †
journal, March 1997
- Kovala, Tom; Sanwal, Bishnu D.; Ball, Eric H.
- Biochemistry, Vol. 36, Issue 10
The Human Cyclic AMP-specific Phosphodiesterase PDE-46 (HSPDE4A4B) Expressed in Transfected COS7 Cells Occurs as Both Particulate and Cytosolic Species That Exhibit Distinct Kinetics of Inhibition by the Antidepressant Rolipram
journal, December 1996
- Huston, Elaine; Pooley, Linda; Julien, Pascale
- Journal of Biological Chemistry, Vol. 271, Issue 49
Crystal structure of phosphodiesterase 4D and inhibitor complex 1
journal, September 2002
- Lee, Mi Eun; Markowitz, Joseph; Lee, Jie-Oh
- FEBS Letters, Vol. 530, Issue 1-3
The regulatory tandem domains of human phosphodiesterases 1 and 4 regulate a cyanobacterial adenylyl cyclase
journal, August 2012
- Banjac, Ana; Kurz, Ursula; Schultz, Joachim E.
- Cellular Signalling, Vol. 24, Issue 8
UCR1 and UCR2 Domains Unique to the cAMP-specific Phosphodiesterase Family Form a Discrete Module via Electrostatic Interactions
journal, March 2000
- Beard, Matthew B.; Olsen, Aileen E.; Jones, Randy E.
- Journal of Biological Chemistry, Vol. 275, Issue 14
Probability-based protein identification by searching sequence databases using mass spectrometry data
journal, December 1999
- Perkins, David N.; Pappin, Darryl J. C.; Creasy, David M.
- Electrophoresis, Vol. 20, Issue 18
Specificity and spatial dynamics of protein kinase A signaling organized by A-kinase-anchoring proteins
journal, February 2010
- Pidoux, Guillaume; Taskén, Kjetil
- Journal of Molecular Endocrinology, Vol. 44, Issue 5
Phosphodiesterases in the CNS: targets for drug development
journal, August 2006
- Menniti, Frank S.; Faraci, W. Stephen; Schmidt, Christopher J.
- Nature Reviews Drug Discovery, Vol. 5, Issue 8
Dimerization of the Type 4 cAMP-specific Phosphodiesterases Is Mediated by the Upstream Conserved Regions (UCRs)
journal, August 2002
- Richter, Wito; Conti, Marco
- Journal of Biological Chemistry, Vol. 277, Issue 43
Identification of PDE4B Over 4D subtype-selective inhibitors revealing an unprecedented binding mode
journal, July 2009
- Kranz, Michael; Wall, Michael; Evans, Brian
- Bioorganic & Medicinal Chemistry, Vol. 17, Issue 14
Epac is a Rap1 guanine-nucleotide-exchange factor directly activated by cyclic AMP
journal, December 1998
- de Rooij, Johan; Zwartkruis, Fried J. T.; Verheijen, Mark H. G.
- Nature, Vol. 396, Issue 6710
Exome Sequencing Identifies PDE4D Mutations in Acrodysostosis
journal, April 2012
- Lee, Hane; Graham, John M.; Rimoin, David L.
- The American Journal of Human Genetics, Vol. 90, Issue 4
Exome Sequencing Identifies PDE4D Mutations as Another Cause of Acrodysostosis
journal, April 2012
- Michot, Caroline; Le Goff, Carine; Goldenberg, Alice
- The American Journal of Human Genetics, Vol. 90, Issue 4
Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety
journal, December 2009
- Burgin, Alex B.; Magnusson, Olafur T.; Singh, Jasbir
- Nature Biotechnology, Vol. 28, Issue 1
Activation of the cAMP-specific Phosphodiesterase PDE4D3 by Phosphorylation: IDENTIFICATION AND FUNCTION OF AN INHIBITORY DOMAIN
journal, July 1999
- Lim, Jaeseung; Pahlke, Gudrun; Conti, Marco
- Journal of Biological Chemistry, Vol. 274, Issue 28
The CCP4 suite programs for protein crystallography
journal, September 1994
- ,
- Acta Crystallographica Section D Biological Crystallography, Vol. 50, Issue 5, p. 760-763
Atomic Structure of PDE4: Insights into Phosphodiesterase Mechanism and Specificity
journal, June 2000
- Xu, R. X.
- Science, Vol. 288, Issue 5472
Long PDE4 cAMP specific phosphodiesterases are activated by protein kinase A-mediated phosphorylation of a single serine residue in Upstream Conserved Region 1 (UCR1): PKA phosphorylation of PDE4 cAMP phosphodiesterases
journal, June 2002
- MacKenzie, Simon J.; Baillie, George S.; McPhee, Ian
- British Journal of Pharmacology, Vol. 136, Issue 3
Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors
journal, November 2007
- Wang, Huanchen; Peng, Ming-Sheng; Chen, Yi
- Biochemical Journal, Vol. 408, Issue 2
Phosphodiesterases as Drug Targets
book, January 2011
- Francis, Sharron H.; Conti, Marco; Houslay, Miles D.
- Handbook of Experimental Pharmacology
Sub-family selective actions in the ability of Erk2 MAP kinase to phosphorylate and regulate the activity of PDE4 cyclic AMP-specific phosphodiesterases: Erk phosphorylation of PDE4 isoenzymes
journal, October 2000
- Baillie, George S.; MacKenzie, Simon J.; McPhee, Ian
- British Journal of Pharmacology, Vol. 131, Issue 4
Cyclic nucleotide research — still expanding after half a century
journal, September 2002
- Beavo, Joseph A.; Brunton, Laurence L.
- Nature Reviews Molecular Cell Biology, Vol. 3, Issue 9
Identification of Novel Mutations Confirms Pde4d as a Major Gene Causing Acrodysostosis : HUMAN MUTATION
journal, November 2012
- Lynch, Danielle C.; Dyment, David A.; Huang, Lijia
- Human Mutation, Vol. 34, Issue 1
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Keynote review: Phosphodiesterase-4 as a therapeutic target
journal, November 2005
- Houslay, Miles D.; Schafer, Peter; Zhang, Kam Y. J.
- Drug Discovery Today, Vol. 10, Issue 22
PDE4 cAMP phosphodiesterases: modular enzymes that orchestrate signalling cross-talk, desensitization and compartmentalization
journal, February 2003
- Houslay, Miles D.; Adams, David R.
- Biochemical Journal, Vol. 370, Issue 1
Complexity and Diversity of Mammalian Adenylyl Cyclases
journal, April 1996
- Sunahara, R. K.; Dessauer, C. W.; Gilman, A. G.
- Annual Review of Pharmacology and Toxicology, Vol. 36, Issue 1
Putting the lid on phosphodiesterase 4
journal, January 2010
- Houslay, Miles D.; Adams, David R.
- Nature Biotechnology, Vol. 28, Issue 1
Cyclic Nucleotide-Gated Channels: Molecular Mechanisms of Activation
journal, April 1999
- Broillet, Marie-Christine; Firestein, Stuart
- Annals of the New York Academy of Sciences, Vol. 868, Issue 1 MOLECULAR AND
Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases
journal, December 2004
- Card, Graeme L.; England, Bruce P.; Suzuki, Yoshihisa
- Structure, Vol. 12, Issue 12
The upstream conserved regions (UCRs) mediate homo- and hetero-oligomerization of type 4 cyclic nucleotide phosphodiesterases (PDE4s)
journal, April 2014
- Xie, Moses; Blackman, Brigitte; Scheitrum, Colleen
- Biochemical Journal, Vol. 459, Issue 3
Data processing and analysis with the autoPROC toolbox
journal, March 2011
- Vonrhein, Clemens; Flensburg, Claus; Keller, Peter
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Physiological concentrations of purines and pyrimidines
journal, January 1994
- Traut, Thomas W.
- Molecular and Cellular Biochemistry, Vol. 140, Issue 1
Heterologous Expression and Purification of Recombinant Rolipram-Sensitive Cyclic AMP-Specific Phosphodiesterases
journal, January 1998
- Salanova, Michele; Jin, S. -L. Catherine; Conti, Marco
- Methods, Vol. 14, Issue 1
Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct
journal, October 2009
- Pandit, J.; Forman, M. D.; Fennell, K. F.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 43
Different mutations in PDE4D associated with developmental disorders with mirror phenotypes
journal, November 2013
- Lindstrand, Anna; Grigelioniene, Giedre; Nilsson, Daniel
- Journal of Medical Genetics, Vol. 51, Issue 1
Structural basis for the design of selective phosphodiesterase 4B inhibitors
journal, March 2014
- Fox, David; Burgin, Alex B.; Gurney, Mark E.
- Cellular Signalling, Vol. 26, Issue 3
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Results of a Phase II Study of the Antidepressant Effect of Rolipram
journal, November 1984
- Zeller, E.; Stief, H.; Pflug, B.
- Pharmacopsychiatry, Vol. 17, Issue 06
Characterization of the structure of a low Km, rolipram-sensitive cAMP phosphodiesterase. Mapping of the catalytic domain.
journal, September 1992
- Jin, S. L.; Swinnen, J. V.; Conti, M.
- Journal of Biological Chemistry, Vol. 267, Issue 26
Works referencing / citing this record:
Genetic Association of Phosphodiesterases With Human Cognitive Performance
journal, February 2019
- Gurney, Mark E.
- Frontiers in Molecular Neuroscience, Vol. 12
Phosphodiesterase 4 inhibitor activates AMPK-SIRT6 pathway to prevent aging-related adipose deposition induced by metabolic disorder
journal, September 2018
- Wang, Zhuoran; Liang, Yaru; Zhang, Lu
- Aging, Vol. 10, Issue 9
Small-molecule allosteric activators of PDE4 long form cyclic AMP phosphodiesterases
journal, June 2019
- Omar, Faisa; Findlay, Jane E.; Carfray, Gemma
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 27
Phenotypic, chemical and functional characterization of cyclic nucleotide phosphodiesterase 4 (PDE4) as a potential anthelmintic drug target
journal, July 2017
- Long, Thavy; Rojo-Arreola, Liliana; Shi, Da
- PLOS Neglected Tropical Diseases, Vol. 11, Issue 7
Small-molecule allosteric activators of PDE4 long form cyclic AMP phosphodiesterases
journal, June 2019
- Omar, Faisa; Findlay, Jane E.; Carfray, Gemma
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 27
Phenotypic Variability in a Family with Acrodysostosis Type 2 Caused by a Novel PDE4D Mutation Affecting the Serine Target of Protein Kinase-A Phosphorylation
journal, December 2017
- Hoppmann, Julia; Gesing, Julia; Silve, Caroline
- Journal of Clinical Research in Pediatric Endocrinology
Memory enhancing effects of BPN14770, an allosteric inhibitor of phosphodiesterase-4D, in wild-type and humanized mice
journal, August 2018
- Zhang, Chong; Xu, Ying; Chowdhary, Anirudh
- Neuropsychopharmacology, Vol. 43, Issue 11