The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis<sup>,</sup>

Huai, Qing; Colicelli, John; Ke, Hengming

doi:10.1021/bi034653e

Cited by 119 publications

(152 citation statements)

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“…On the other hand, recent study on the PDE4-AMP structure showed that the metal also interacts with the phosphate oxygen and thus strongly suggests a catalytic role. 10 The strong anomalous scattering at the wavelength of the zinc absorption edge suggests the first metal is a zinc, and is consistent with the fact that zinc, at low concentration, activates the enzyme. 9 In PDE4D2, the second metal ion coordinates with D318, a bound water, and possibly with the phosphate group of the substrate.…”

Section: Introductionsupporting

confidence: 63%

Implications of PDE4 structure on inhibitor selectivity across PDE families

2004

Int J Impot Res

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Phosphodiesterases (PDEs) control cellular concentrations of cyclic adenosine monophosphate (cAMP) or cyclic guanosine monophosphate (cGMP). PDE4 and PDE5 selectively hydrolyze cAMP and cGMP, respectively. PDE family members share approximately 25% sequence identity within a conserved catalytic domain of about 300 amino acids. Crystal structure analysis of PDE4's catalytic domain identifies two metal-binding sites: a high-affinity site and a low-affinity site, which probably bind zinc (Zn 2 þ ) and magnesium (Mg 2 þ ), respectively. Absolute conservation among the PDEs of two histidine and two aspartic acid residues for divalent metal binding suggests the importance of these amino acids in catalysis. Although active sites of PDEs are apparently structurally similar, PDE4 is specifically inhibited by selective inhibitors such as rolipram, while PDE5 is preferentially blocked by sildenafil. Modeling interactions of the PDE5 inhibitor sildenafil with the PDE4 active site may help explain inhibitor selectivity and provide useful information for the design of new inhibitors.

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Section: Introductionsupporting

confidence: 63%

Implications of PDE4 structure on inhibitor selectivity across PDE families

2004

Int J Impot Res

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“…The superposition of PDE4D2-cAMP over PDE4D-AMP and PDE4B-AMP (18,21,28) yielded the small RMSDs of 0.26-0.73 Å, indicating overall similarity of the structures. In addition, the structural comparison shows some features shared by AMP and cAMP.…”

Section: Product Amp Does Not Simulate Binding Of Substrate Campmentioning

confidence: 95%

“…The cDNA for expression of the catalytic domain of the wild type PDE4D2 was purchased from ATCC (American Type Culture Collection, ATCC #5654749) and subcloned into pET15b, as described previously (21). The plasmid pET-PDE4D for expression of the wild type PDE4D2 (residues 86-413) was mutated to pET-D201N with the QuickChange sitedirected mutagenesis kit (Stratagene) using the PCR primers of 5′-GCCAGTGCAATACATAATGTAGATCATCCTGG-3′ and 5′-CCAGGATGATCTACATTATGTATTGCACTGGC-3′.…”

Section: Protein Expression Crystallization and Structure Determinationmentioning

confidence: 99%

“…First, a phosphate oxygen of AMP bridges two divalent metal ions, but cAMP does not directly contact the metal ions. Second, the side chain of Asn321 in the PDE4-product complexes (18,21,28) changes its conformation to form two hydrogen bonds with N 6 and N7 of AMP. In comparison, Asn321 in the PDE4D2-cAMP complex retains its conformation in the unliganded state and does not form hydrogen bonds with cAMP.…”

Section: Product Amp Does Not Simulate Binding Of Substrate Campmentioning

confidence: 99%

“…In comparison, Asn321 in the PDE4D2-cAMP complex retains its conformation in the unliganded state and does not form hydrogen bonds with cAMP. Finally, two hydrogen bonds are formed between N1 and N 6 of AMP and Ne2 and Oe1 of Gln369 in the PDE4-product complexes (18,21,28). In contrast, Gln369 in the PDE4D2-cAMP structure forms only one hydrogen bond with N1 of cAMP, and …”

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The Molecular Basis for Different Recognition of Substrates by Phosphodiesterase Families 4 and 10

Wang

Robinson

2007

Journal of Molecular Biology

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SummaryPhosphodiesterases (PDEs) are key enzymes that control the cellular concentrations of the second messengers cAMP and cGMP. The mechanism for selective recognition of substrates cAMP and cGMP by individual PDE families remains a puzzle. To understand the mechanism for substrate recognition by PDE enzymes, the crystal structure of the catalytic domain of an inactive D201N mutant of PDE4D2 in complex with substrate cAMP has been determined at 1.56 Å resolution. The structure shows that Gln369 forms only one hydrogen bond with the adenine of cAMP. This finding provides experimental evidence against the hypothesis of two hydrogen bonds between the invariant glutamine and the substrate cAMP in PDE4, and thus suggests that the widely circulated "glutamine switch" model is unlikely the mechanism for substrate recognition by PDEs. A structure comparison between PDE4D2-cAMP and PDE10A2-cAMP reveals an anti configuration of cAMP in PDE4D2 but syn in PDE10A2, in addition to different contact patterns of cAMP in these two structures. These observations imply that individual PDE families have their characteristic mechanisms for substrate recognition. KeywordsPDE4; cAMP/cGMP; substrate specificity Cyclic nucleotide phosphodiesterases (PDEs) regulate the cellular concentrations of the second messengers cAMP and cGMP and play important roles in many biological processes (1-7). The human genome encodes twenty-one PDE genes that are categorized into eleven families. Alternative mRNA splicing of the PDE genes produces about one hundred proteins (1,3). Selective inhibitors against individual PDE families have been widely studied as therapeutics for treatment of various human diseases (8-15). For example, the PDE5 selective inhibitor sildenafil has been approved for treatment of male erectile dysfunction and pulmonary hypertension (16,17).Individual PDE families have different specificities in hydrolysis of substrates cAMP and cGMP. Thus, PDE families of 4, 7, and 8 prefer to hydrolyze cAMP while PDE5, 6, and 9 are * Correspondence should be addressed to Hengming Ke, Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC 27599-7260, USA, Tel: +1-919-966-2244; Fax: +1-919-966-2852; email: hke@med.unc.edu.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Accession codesThe coordinates and structural factors have been deposited into the Protein Data Bank with accession code of 2PW3. cGMP specific. The remaining PDE families 1, 2, 3, 10, and 11 utilize both cAMP and cGMP as substrates, but have slightly different catalytic efficacies. Understanding subst...

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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 Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis^,

Cited by 119 publications

References 47 publications

Implications of PDE4 structure on inhibitor selectivity across PDE families

Implications of PDE4 structure on inhibitor selectivity across PDE families

The Molecular Basis for Different Recognition of Substrates by Phosphodiesterase Families 4 and 10

Crystal Structures of Phosphodiesterases and Implication on Discovery of Inhibitors

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The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis,

Cited by 119 publications

References 47 publications

Implications of PDE4 structure on inhibitor selectivity across PDE families

Implications of PDE4 structure on inhibitor selectivity across PDE families

The Molecular Basis for Different Recognition of Substrates by Phosphodiesterase Families 4 and 10

Crystal Structures of Phosphodiesterases and Implication on Discovery of Inhibitors

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The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase Catalysis^,