Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B Complexed with AMP, 8-Br-AMP, and Rolipram

Xu, Renfeng; Rocque, Warren J.; Lambert, Millard H.; Vanderwall, Dana E.; Luther, Michael A.; Nolte, R.T.

doi:10.1016/j.jmb.2004.01.040

Cited by 118 publications

(149 citation statements)

References 34 publications

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“…The occupancy of the anti AMP and GMP at the active site in the crystals may reflect the forced binding of the products at high concentration because they are predominant in solution (39). This argument is supported by the fact that only the syn configuration of 8-bromo-AMP was observed in the crystal when its syn configuration is predominant in solution (24,39).…”

Section: Discussionmentioning

confidence: 96%

“…Individual PDE families show different substrate preferences. Crystal structures have been reported for the catalytic domains of seven PDE families in the unliganded form or in complex with inhibitors or products: PDE1B, PDE2A, PDE3B, PDE4B/4D, PDE5A, PDE7A, and PDE9A (22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34). However, it remains a puzzle how the conserved catalytic pocket of the PDE families selectively recognizes cAMP and cGMP.…”

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confidence: 99%

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Structural insight into substrate specificity of phosphodiesterase 10

Wang

Liu

Hou

et al. 2007

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

103

139

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Phosphodiesterases (PDEs) hydrolyze the second messengers cAMP and cGMP. It remains unknown how individual PDE families selectively recognize cAMP and cGMP. This work reports structural studies on substrate specificity. The crystal structures of the catalytic domains of the D674A and D564N mutants of PDE10A2 in complex with cAMP and cGMP reveal that two substrates bind to the active site with the same syn configuration but different orientations and interactions. The products AMP and GMP bind PDE10A2 with the anti configuration and interact with both divalent metals, in contrast to no direct contact of the substrates. The structures suggest that the syn configurations of cAMP and cGMP are the genuine substrates for PDE10 and the specificity is achieved through the different interactions and conformations of the substrates. The PDE10A2 structures also show that the conformation of the invariant glutamine is locked by two hydrogen bonds and is unlikely to switch for substrate recognition. Sequence alignment shows a potential pocket, in which variation of amino acids across PDE families defines the size and shape of the pocket and thus determines the substrate specificity.crystal structure ͉ cyclic nucleotides cAMP and cGMP C yclic nucleotide phosphodiesterases (PDEs) are enzymes hydrolyzing the second messengers adenosine and guanosine 3Ј,5Ј-cyclic monophosphates (cAMP and cGMP). The human genome encodes 21 PDE genes that are categorized into 11 families (1, 2). Selective inhibitors against individual PDE families have been developed as therapeutics for treatment of various human diseases (3-8). The best known examples are the PDE5 inhibitors sildenafil (Viagra), vardenafil (Levitra), and tadalafil (Cialis) that have been used for treatment of male erectile dysfunction (5). Sildenafil (Revatio) has also been approved for treatment of pulmonary hypertension (9). PDE10 was independently identified by three groups in 1999 and shows a dual activity on hydrolysis of both cAMP and cGMP (10-12). PDE10 is highly expressed in brain striatum (13-16). Reduction of PDE10A mRNA and protein levels in striatum of transgenic mice implies a role of PDE10A in Huntington's disease (17,18). Knockout mice experiments suggest that PDE10A is involved in regulating striatal output, possibly by reducing the sensitivity of medium spiny neurons to glutamatergic excitation (19). The PDE10 inhibitor papaverine is effective in improving executive function deficits associated with schizophrenia, and therefore inhibition of PDE10 may represent an approach to treatment of psychosis (20,21).PDE families contain a variable N-terminal regulatory domain and a conserved C-terminal catalytic domain. Individual PDE families show different substrate preferences. Crystal structures have been reported for the catalytic domains of seven PDE families in the unliganded form or in complex with inhibitors or products: PDE1B, PDE2A, PDE3B, PDE4B/4D, PDE5A, PDE7A, and PDE9A (22-34). However, it remains a puzzle how the conserved catalytic pocket of the PDE famili...

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Section: Discussionmentioning

confidence: 96%

mentioning

confidence: 99%

Structural insight into substrate specificity of phosphodiesterase 10

Wang

Liu

Hou

et al. 2007

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

103

139

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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: 96%

“…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 …”

Section: Product Amp Does Not Simulate Binding Of Substrate Campmentioning

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%

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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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Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B Complexed with AMP, 8-Br-AMP, and Rolipram

Cited by 118 publications

References 34 publications

Structural insight into substrate specificity of phosphodiesterase 10

Structural insight into substrate specificity of phosphodiesterase 10

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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