Naunyn-Schmiedeberg's Archives of Pharmacology

, Volume 392, Issue 2, pp 199–208 | Cite as

Hydrolysis of the non-canonical cyclic nucleotide cUMP by PDE9A: kinetics and binding mode

  • Jessica Scharrenbroich
  • Volkhard Kaever
  • Stefan Dove
  • Roland Seifert
  • Erich H. SchneiderEmail author
Original Article


The non-canonical cyclic nucleotide cUMP and the phosphodiesterase PDE9A both occur in neuronal cells. Using HPLC-coupled tandem mass spectrometry, we characterized the kinetics of PDE9A-mediated cUMP hydrolysis. PDE9A is a low-affinity and high-velocity enzyme for cUMP (Vmax = ~ 6 μmol/min/mg; Km = ~ 401 μM). The PDE9 inhibitor BAY 73-6691 inhibited PDE9A-catalyzed cUMP hydrolysis (Ki = 590 nM). Docking studies indicate two H-bonds between the cUMP uridine moiety and Gln453/Asn405 of PDE9A. By contrast, the guanosine moiety of cGMP forms three H-bonds with Gln453. cCMP is not hydrolyzed at a concentration of 3 μM, but inhibits the PDE9A-catalyzed cUMP hydrolysis at concentrations of 100 μM or more. The probable main reason is that the cytosine moiety cannot act as H-bond acceptor for Gln453. A comparison of PDE9A with PDE7A suggests that the preference of the former for cGMP and cUMP and of the latter for cAMP and cCMP is due to stabilized alternative conformations of the side chain amide of Gln453 and Gln413, respectively. This so-called glutamine switch is known to be involved in the regulation of cAMP/cGMP selectivity of some PDEs.


Cyclic UMP Cyclic CMP Phosphodiesterase PDE9A Enzyme kinetics Glutamine switch 



Bovine serum albumin


Adenosine 3′,5′-cyclic monophosphate


Cytidine 3′,5′-cyclic monophosphate


Guanosine 3′,5′-cyclic monophosphate


Cytidine 5′-monophosphate


Nucleoside 3′,5′-cyclic monophosphate


Uridine 3′,5′-cyclic monophosphate


Ethylenediaminetetraacetic acid


Exotoxin of Pseudomonas aeruginosa with nucleotidyl cyclase properties


Guanosine 5′-monophosphate


Glutathione S-transferase (used as protein tag)


Hyperpolarization-activated cyclic nucleotide-gated channel


High-performance liquid chromatography-coupled tandem mass spectrometry




Michaelis-Menten constant


Multidrug resistance-associated protein


Nucleoside 5′-monophosphate




Protein kinase A


Protein kinase G


Soluble adenylyl cyclase


Standard deviation


Standard error of the mean


Soluble guanylyl cyclase


Uridine 5′-monophosphate


Maximum velocity of an enzymatic reaction under saturating conditions



We thank Prof. Dr. Martin Stangel (Dept. of Clinical Neuroimmunology and Neurochemistry, MHH) and Dr. Sabine Wolter (Institute of Pharmacology, MHH) for the excellent scientific discussions as well as Mrs. Annette Garbe (Research Core Unit Metabolomics, MHH) for the outstanding technical support.

Author contributions

Participated in research design: Schneider, Scharrenbroich, Seifert

Conducted experiments: Scharrenbroich, Kaever

Performed data analysis: Scharrenbroich, Schneider

Performed docking approaches: Dove

Wrote or contributed to the writing of the manuscript: Scharrenbroich, Schneider, Dove, Kaever, Seifert


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Hannover Medical SchoolInstitute of PharmacologyHannoverGermany
  2. 2.Research Core Unit Metabolomics, Hannover Medical SchoolInstitute of PharmacologyHannoverGermany
  3. 3.Department of Medicinal Chemistry II, Institute of PharmacyUniversity of RegensburgRegensburgGermany

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