Structural determinants for inhibitor specificity and selectivity in PDE2A using the wheat germ in vitro translation system

Biochemistry

Volumn 44, Issue 23, 2005, Pages 8312-8325

  Iffland, André ^a,b   Kohls, Darcy ^a   Low, Simon ^a   Luan, Jing ^a   Zhang, Yan ^a   Kothe, Michael ^a   Cao, Qing ^a   Kamath, Ajith V ^a   Ding, Yuan Hua ^a   Ellenberger, Tom ^b,c  

^a PFIZER GLOBAL RESEARCH AND DEVELOPMENT   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c Department of Biological Chemistry and Molecular Pharmacology ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARDIAC CONTRACTILITY; MUSCLE CONTRACTION; PHOSPHODIESTERASES; STRUCTURAL DETERMINANTS;

AGGLOMERATION; CELLS; DISEASES; DRUG PRODUCTS; PURIFICATION; SIGNALING;

ENZYME INHIBITION;

ASPARTIC ACID; ATRIAL NATRIURETIC FACTOR; CYCLIC GMP; CYCLIC NUCLEOTIDE; GLYCINE; ISOLEUCINE; PHOSPHODIESTERASE; PHOSPHODIESTERASE 2; PHOSPHODIESTERASE 2A; PHOSPHODIESTERASE INHIBITOR; ROLIPRAM; TYROSINE; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BLOOD PRESSURE REGULATION; BRAIN TISSUE; CELL FREE SYSTEM; DRUG DESIGN; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME SUBSTRATE; FLUID BALANCE; GENE MUTATION; GENE OVEREXPRESSION; GLYCOGENOLYSIS; HEART; HEART MUSCLE CONTRACTILITY; HUMAN; HUMAN CELL; IN VITRO STUDY; INHIBITION KINETICS; LIPOLYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; RNA TRANSLATION; SENSITIVITY AND SPECIFICITY; SMOOTH MUSCLE CONTRACTION; STRUCTURE ANALYSIS; THROMBOCYTE AGGREGATION; TISSUE DISTRIBUTION; WHEAT GERM;

3',5'-CYCLIC-GMP PHOSPHODIESTERASE; 3',5'-CYCLIC-NUCLEOTIDE PHOSPHODIESTERASE; ADENINE; AMINO ACID SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; CELL-FREE SYSTEM; CRYSTALLOGRAPHY, X-RAY; HUMANS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PHOSPHODIESTERASE INHIBITORS; PROTEIN BINDING; PROTEIN BIOSYNTHESIS; ROLIPRAM; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY; TRITICUM;

TRITICUM AESTIVUM;

EID: 20444363484     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047313h     Document Type: Article

References (44)

1. Houslay, M. D., and Milligan, G. (1997) Tailoring cAMP-signalling responses through isoform multiplicity. Trends Biochem. Sci. 22, 217-24.
2. Houslay, M. D., Sullivan, M., and Bolger, G. B. (1998) The multienzyme PDE4 cyclic adenosine monophosphate-specific phosphodiesterase family: intracellular targeting, regulation, and selective inhibition by compounds exerting anti-inflammatory and antidepressant actions, Adv. Pharmacol. 44, 225-342.
3. Beavo, J. A. (1995) Cyclic nucleotide phosphodiesterases: functional implications of multiple isoforms, Physiol. Rev. 75, 725-48.
4. Conti, M. (2000) Phosphodiesterases and cyclic nucleotide signaling in endocrine cells, Mol. Endocrinol. 14, 1317-27.
5. Charbonneau, H., Beier, N., Walsh, K. A., and Beavo, J. A. (1986) Identification of a conserved domain among cyclic nucleotide phosphodiesterases from diverse species, Proc. Natl. Acad. Sci. U.S.A. 83, 9308-12.
6. Francis, S. H., Colbran, J. L., McAllister-Lucas, L. M., and Corbin, J. D. (1994) Zinc interactions and conserved motifs of the cGMP-binding cGMP-specific phosphodiesterase suggest that it is a zinc hydrolase. J. Biol. Chem. 269, 22477-80.
7. Manganiello, V. C., Murata, T., Taira, M., Beifrage, P., and Degerman, E. (1995) Diversity in cyclic nucleotide phosphodiesterase isoenzyme families, Arch. Biochem. Biophys. 322, 1-13.
8. Corbin, J. D., Francis, S. H., and Webb, D. J. (2002) Phosphodiesterase type 5 as a pharmacologic target in erectile dysfunction, Urology 60, 4-11.
9. Rosen, R. C., and Kostis, J. B. (2003) Overview of phosphodiesterase 5 inhibition in erectile dysfunction, Am. J. Cardiol. 92, 9M-18M.
10. Rosman, G. J., Martins, T. J., Sonnenburg, W. K., Beavo, J. A., Ferguson, K., and Loughney, K. (1997) Isolation and characterization of human cDNAs encoding a cGMP-stimulated 3′,5′-cyclic nucleotide phosphodiesterase, Gene 191, 89-95.
11. Martinez, S. E., Wu, A. Y., Glavas, N. A., Tang, X. B., Turley, S., Hol, W. G., and Beavo, J. A. (2002) The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding, Proc. Natl. Acad. Sci. U.S.A. 99, 13260-5.
12. Aravind, L., and Ponting, C. P. (1997) The GAF domain: an evolutionary link between diverse phototransducing proteins, Trends Biochem. Sci. 22, 458-9.
13. Torphy, T. J., Stadel, J. M., Burman, M., Cieslinski, L. B., McLaughlin, M. M., White, J. R., and Livi, G. P. (1992) Coexpression of human cAMP-specific phosphodiesterase activity and high affinity rolipram binding in yeast. J. Biol. Chem. 267, 1798-804.
14. Hayashi, M, Matsushima, K., Ohashi, H., Tsunoda, H., Murase, S., Kawarada, Y., and Tanaka, T. (1998) Molecular cloning and characterization of human PDE8B, a novel thyroid-specific isozyme of 3′,5′-cyclic nucleotide phosphodiesterase, Biochem. Biophys. Res. Commun. 250, 751-6.
15. Hetman, J. M., Soderling, S. H., Glavas, N. A., and Beavo, J. A. (2000) Cloning and characterization of PDE7B, a cAMP-specific phosphodiesterase, Proc. Natl. Acad. Sci. U.S.A. 97, 472-6.
16. Soderling, S. H., Bayuga, S. J., and Beavo, J. A. (1998) Cloning and characterization of a cAMP-specific cyclic nucleotide phosphodiesterase, Proc. Natl. Acad. Sci. U.S.A. 95, 8991-6.
17. Fisher, D. A., Smith, J. F., Pillar, J. S., St Denis, S. H., and Cheng, J. B. (1998) Isolation and characterization of PDE9A, a novel human cGMP-specific phosphodiesterase, J. Biol. Chem. 273, 15559-64.
18. Hetman, J. M., Robas, N., Baxendale, R., Fidock, M., Phillips, S. C., Soderling, S. H., and Beavo, J. A. (2000) Cloning and characterization of two splice variants of human phosphodiesterase 11A, Proc. Natl. Acad. Sci. U.S.A. 97, 12891-5.
19. MacFarland, R. T., Zelus, B. D., and Beavo, J. A. (1991) High concentrations of a cGMP-stimulated phosphodiesterase mediate ANP-induced decreases in cAMP and steroidogenesis in adrenal glomerulosa cells, J. Biol. Chem. 266, 136-42.
20. Huai, Q., Wang, H., Sun, Y., Kim, H. Y., Liu, Y., and Ke, H. (2003) Three-dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity, Structure (Cambridge, MA, U.S.) 11, 865-73.
21. Schilling, R. J., Morgan, D. R., and Kilpatrick, B. F. (1994) A high-throughput assay for cyclic nucleotide phosphodiesterases, Anal. Biochem. 216, 154-8.
22. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal. Biochem. 72, 248-54.
23. Kozak, M. (1991) Effects of long 5′ leader sequences on initiation by eukaryotic ribosomes in vitro, Gene Expression 1, 117-25.
24. Kozak, M. (1988) Leader length and secondary structure modulate mRNA function under conditions of stress. Mol. Cell. Biol. 8, 2737-44.
25. Johnson, J. D., Walters, J. D., and Mills, J. S. (1987) A continuous fluorescence assay for cyclic nucleotide phosphodiesterase hydrolysis of cyclic GMP, Anal. Biochem. 162, 291-5.
26. Otwinowski, Z., and Minor, W. (1997) Processing of X-Ray Diffraction Data Collected in Oscillation Mode, Methods Enzymol. 276, 307-26.
27. Kissinger, C. R., Gehlhaar, D. K., and Fogel, D. B. (1999) Rapid automated molecular replacement by evolutionary search, Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 (Part 2), 484-91.
28. Xu, R. X., Hassell, A. M., Vanderwall, D., Lambert, M. H., Holmes, W. D., Luther, M. A., Rocque, W. J., Milburn, M. V., Zhao, Y., Ke, H., and Nolle, R. T. (2000) Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity, Science 288, 1822-5.
29. Murshudov, G. N., Vagin, A. A., Lebedev, A., Wilson, K. S., and Dodson, E. J. (1999) Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 (Part 1), 247-55.
30. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr., Sect. A 47 (Part 2), 110-9.
31. Huai, Q., Colicelli, J., and Ke, H. (2003) The crystal structure of AMP-bound PDE4 suggests a mechanism for phosphodiesterase catalysis. Biochemistry 42, 13220-6.
32. Mumby, M. C., Martins, T. J., Chang, M. L., and Beavo, J. A. (1982) Identification of cGMP-stimulated cyclic nucleotide phosphodiesterase in lung tissue with monoclonal antibodies. J. Biol. Chem. 257, 13283-90.
33. Essayan, D. M. (1999) Cyclic nucleotide phosphodiesterase (PDE) inhibitors and immunomodulation, Biochem. Pharmacol. 57, 965-73.
34. Zhang, K. Y., Card, G. L., Suzuki, Y., Artis, D. R., Fong, D., Gillette, S., Hsieh, D., Neiman, J., West, B. L., Zhang, C., Milburn, M. V., Kim, S. H., Schlessinger, J., and Bollag, G. (2004) A Glutamine Switch Mechanism for Nucleotide Selectivity by Phosphodiesterases, Mol. Cell 15, 279-86.
35. Scapin, G., Patel, S. B., Chung, C., Varnerin, J. P., Edmondson, S. D., Mastracchio, A., Parmee, E. R., Singh, S. B., Becker, J. W., Van der Ploeg, L. H., and Tota, M. R. (2004) Crystal structure of human phosphodiesterase 3B: atomic basis for substrate and inhibitor specificity, Biochemistry 43, 6091-100.
36. Huai, Q., Wang, H., Zhang, W., Colman, R. W., Robinson, H., and Ke, H. (2004) Crystal structure of phosphodiesterase 9 shows orientation variation of inhibitor 3-isobutyl-1-methylxanthine binding, Proc. Natl. Acad. Sci. U.S.A. 101, 9624-9.
37. Huai, Q., Liu, Y., Francis, S. H., Corbin, J. D., and Ke, H. (2004) Crystal structures of phosphodiesterases 4 and 5 in complex with inhibitor 3-isobutyl-1-methylxanthine suggest a conformation determinant of inhibitor selectivity. J. Biol. Chem. 279, 13095-101.
38. Card, G. L., England, B. P., Suzuki, Y., Fong, D., Powell, B., Lee, B., Luu, C., Tabrizizad, M., Gillette, S., Ibrahim, P. N., Artis, D. R., Bollag, G., Milburn, M. V., Kim, S. H., Schlessinger, J., and Zhang, K. Y. (2004) Structural basis for the activity of drugs that inhibit phosphodiesterases, Structure (Cambridge, MA, U.S.) 12, 2233-47.
39. Xu, R. X., Rocque, W. J., Lambert, M. H., Vanderwall, D. E., Luther, M. A., and Nolle, R. T. (2004) Crystal structures of the catalytic domain of phosphodiesterase 4B complexed with AMP, 8-Br-AMP, and rolipram, J. Mol. Biol. 337, 355-65.
40. Fujishige, K., Kotera, J., Michibata, H., Yuasa, K., Takebayashi, S., Okumura, K., and Omori, K. (1999) Cloning and characterization of a novel human phosphodiesterase that hydrolyzes both cAMP and cGMP (PDE10A), J. Biol. Chem. 274, 18438-45.
41. Soderling, S. H., Bayuga, S. J., and Beavo, J. A. (1999) Isolation and characterization of a dual-substrate phosphodiesterase gene family: PDE10A, Proc. Natl. Acad. Sci. U.S.A. 96, 7071-6.
42. Richter, W., Unciuleac, L., Hermsdorf, T., Kronbach, T., and Dettmer, D. (2001) Identification of inhibitor binding sites of the cAMP-specific phosphodiesterase 4, Cell. Signalling 13, 287-97.
43. Richter, W., Unciuleac, L., Hermsdorf, T., Kronbach, T., and Dettmer, D. (2001) Identification of substrate specificity determinants in human cAMP-specific phosphodiesterase 4A by single-point mutagenesis, Cell. Signalling 13, 159-67.
44. Card, G. L., Blasdel, L., England, B. P., Zhang, C., Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P. N., Artis, D. R., Bollag, G., Milburn, M. V., Kim, S. H., Schlessinger, J., and Zhang, K. Y. (2005) A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design, Nat. Biotechnol. 23, 201-7.