The Structure of the GAF A Domain from Phosphodiesterase 6C Reveals Determinants of cGMP Binding, a Conserved Binding Surface, and a Large cGMP-dependent Conformational Change

Martinez, Sergio E.; Heikaus, Clemens C.; Klevit, Rachel E.; Beavo, Joseph A.

doi:10.1074/jbc.m802891200

Cited by 44 publications

(69 citation statements)

References 49 publications

(48 reference statements)

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“…GAF-A and GAF-B have similar overall topology that is also similar to those of the published GAF domain structures, namely, the GAF domains from yeast YKG9, mouse PDE2A, Cyanobacterium anabena adenylate cyclase, PDE5 GAF-A, PDE6 GAF-A, and PDE10 GAF-B (25)(26)(27)(28)(29)(30). Each domain contains a six-stranded antiparallel ␤-sheet (␤3-␤2-␤1-␤6-␤5-␤4) sandwiched by a three-helix bundle (␣1, ␣2, and ␣5) on one side and two short ␣-helices (␣3 and ␣4) on the other.…”

Section: Resultsmentioning

confidence: 55%

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Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct

Pandit

Forman

Fennell

et al. 2009

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

150

159

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We report the X-ray crystal structure of a phosphodiesterase (PDE) that includes both catalytic and regulatory domains. PDE2A (215-900) crystallized as a dimer in which each subunit had an extended organization of regulatory GAF-A and GAF-B and catalytic domains connected by long ␣-helices. The subunits cross at the GAF-B/ catalytic domain linker, and each side of the dimer contains in series the GAF-A and GAF-B of one subunit and the catalytic domain of the other subunit. A dimer interface extends over the entire length of the molecule. The substrate binding pocket of each catalytic domain is occluded by the H-loop. We deduced from comparisons with structures of isolated, ligand-bound catalytic subunits that the H-loop swings out to allow substrate access. However, in dimeric PDE2A (215-900), the H-loops of the two catalytic subunits pack against each other at the dimer interface, necessitating movement of the catalytic subunits to allow for H-loop movement. Comparison of the unliganded GAF-B of PDE2A (215-900) with previous structures of isolated, cGMP-bound GAF domains indicates that cGMP binding induces a significant shift in the GAF-B/catalytic domain linker. We propose that cGMP binding to GAF-B causes movement, through this linker region, of the catalytic domains, such that the H-loops no longer pack at the dimer interface and are, instead, free to swing out to allow substrate access. This increase in substrate access is proposed as the basis for PDE2A activation by cGMP and may be a general mechanism for regulation of all PDEs.cGMP activation ͉ GAF domains ͉ PDE-2A T he cyclic nucleotides cAMP and cGMP are ubiquitous intracellular signaling molecules that mediate a vast array of biological processes throughout the body. The means by which these two molecules participate in diverse functions, in different cell types and within single cells, involves tight regulation of the spatial and temporal residence of their concentrations. The phosphodiesterases (PDEs) are a superfamily of enzymes that metabolically inactivate cAMP and cGMP (1) to play key roles in both these aspects of regulation. The PDEs are modular enzymes characterized by a relatively conserved C-terminal catalytic domain and a more variable N-terminal domain involved in regulation of activity, subcellular localization, and interactions with other proteins. There are 11 PDE gene families, with different families encoded by one to four genes, and further diversity derived from alternative splicing. The PDE families differ broadly in specificity and affinity for cAMP and cGMP. Much has been learned about the molecular bases for these differences from studies of X-ray crystal structures of the catalytic domains of

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Section: Resultsmentioning

confidence: 55%

“…2B). All crystal structures of nucleotide-bound GAF domains show the nucleotide to be completely buried (25)(26)(27)(28)(29)(30). Helix ␣4 and the loop connecting strands ␤2 and ␤3 are fully ordered and are ''clamped down'' on the nucleotide, making multiple specific interactions.…”

Section: Resultsmentioning

confidence: 99%

Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct

Pandit

Forman

Fennell

et al. 2009

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

150

159

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“…In PDE6␣␤, high affinity and selectivity for heterodimerization between the monomers requires a single ␣-helix (␣1) (266). However, in the recently determined structure for GAF-A from PDE6␣=, this helix is similarly positioned to that in GAF-B of PDE2, but it is a monomer (232).…”

Section: Dimerization Of Gaf-containing Phosphodiesterasesmentioning

confidence: 99%

“…Subsequent studies with other PDE GAFs have revealed that there is no pattern for involvement of a GAF in dimerization and/or cN binding ( Fig. 2) (137,141,142,232,333). Monomers within GAF-containing PDEs are arranged in parallel; dimerization involves multiple regions and is uniquely mediated among PDEs (179,182,232,233,437).…”

Section: Dimerization Of Gaf-containing Phosphodiesterasesmentioning

confidence: 99%

“…2) (137,141,142,232,333). Monomers within GAF-containing PDEs are arranged in parallel; dimerization involves multiple regions and is uniquely mediated among PDEs (179,182,232,233,437). GAFs that appear to be involved in dimerization include GAF-A in PDEs 2, 5, and 10 (137,142,233) as well as GAF-B in PDEs 2, 5, and 10 (137, 437).…”

Section: Dimerization Of Gaf-containing Phosphodiesterasesmentioning

confidence: 99%

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Mammalian Cyclic Nucleotide Phosphodiesterases: Molecular Mechanisms and Physiological Functions

Francis

Blount

Corbin

2011

Physiological Reviews

560

546

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The superfamily of cyclic nucleotide (cN) phosphodiesterases (PDEs) is comprised of 11 families of enzymes. PDEs break down cAMP and/or cGMP and are major determinants of cellular cN levels and, consequently, the actions of cN-signaling pathways. PDEs exhibit a range of catalytic efficiencies for breakdown of cAMP and/or cGMP and are regulated by myriad processes including phosphorylation, cN binding to allosteric GAF domains, changes in expression levels, interaction with regulatory or anchoring proteins, and reversible translocation among subcellular compartments. Selective PDE inhibitors are currently in clinical use for treatment of erectile dysfunction, pulmonary hypertension, intermittent claudication, and chronic pulmonary obstructive disease; many new inhibitors are being developed for treatment of these and other maladies. Recently reported x-ray crystallographic structures have defined features that provide for specificity for cAMP or cGMP in PDE catalytic sites or their GAF domains, as well as mechanisms involved in catalysis, oligomerization, autoinhibition, and interactions with inhibitors. In addition, major advances have been made in understanding the physiological impact and the biochemical basis for selective localization and/or recruitment of specific PDE isoenzymes to particular subcellular compartments. The many recent advances in understanding PDE structures, functions, and physiological actions are discussed in this review.

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Crystal Structures of Phosphodiesterases and Implication on Discovery of Inhibitors

Wang

et al. 2014

Cyclic‐Nucleotide Phosphodiesterases in the Central Nervous System

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The Structure of the GAF A Domain from Phosphodiesterase 6C Reveals Determinants of cGMP Binding, a Conserved Binding Surface, and a Large cGMP-dependent Conformational Change

Cited by 44 publications

References 49 publications

Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct

Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct

Mammalian Cyclic Nucleotide Phosphodiesterases: Molecular Mechanisms and Physiological Functions

Crystal Structures of Phosphodiesterases and Implication on Discovery of Inhibitors

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