3ECN
Crystal structure of PDE8A catalytic domain in complex with IBMX
Summary for 3ECN
| Entry DOI | 10.2210/pdb3ecn/pdb |
| Related | 3ECM |
| Descriptor | High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A, 3-ISOBUTYL-1-METHYLXANTHINE, ZINC ION, ... (5 entities in total) |
| Functional Keywords | ibmx, pde8a catalytic domain, refolding, alternative splicing, camp, hydrolase, magnesium, manganese, metal-binding |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 2 |
| Total formula weight | 78803.96 |
| Authors | |
| Primary citation | Wang, H.,Yan, Z.,Yang, S.,Cai, J.,Robinson, H.,Ke, H. Kinetic and structural studies of phosphodiesterase-8A and implication on the inhibitor selectivity Biochemistry, 47:12760-12768, 2008 Cited by PubMed Abstract: Cyclic nucleotide phosphodiesterase-8 (PDE8) is a family of cAMP-specific enzymes and plays important roles in many biological processes, including T-cell activation, testosterone production, adrenocortical hyperplasia, and thyroid function. However, no PDE8 selective inhibitors are available for trial treatment of human diseases. Here we report kinetic properties of the highly active PDE8A1 catalytic domain prepared from refolding and its crystal structures in the unliganded and 3-isobutyl-1-methylxanthine (IBMX) bound forms at 1.9 and 2.1 A resolutions, respectively. The PDE8A1 catalytic domain has a K(M) of 1.8 microM, V(max) of 6.1 micromol/min/mg, a k(cat) of 4.0 s(-1) for cAMP, and a K(M) of 1.6 mM, V(max) of 2.5 micromol/min/mg, a k(cat) of 1.6 s(-1) for cGMP, thus indicating that the substrate specificity of PDE8 is dominated by K(M). The structure of the PDE8A1 catalytic domain has similar topology as those of other PDE families but contains two extra helices around Asn685-Thr710. Since this fragment is distant from the active site of the enzyme, its impact on the catalysis is unclear. The PDE8A1 catalytic domain is insensitive to the IBMX inhibition (IC(50) = 700 microM). The unfavorable interaction of IBMX in the PDE8A1-IBMX structure suggests an important role of Tyr748 in the inhibitor binding. Indeed, the mutation of Tyr748 to phenylalanine increases the PDE8A1 sensitivity to several nonselective or family selective PDE inhibitors. Thus, the structural and mutagenesis studies provide not only insight into the enzymatic properties but also guidelines for design of PDE8 selective inhibitors. PubMed: 18983167DOI: 10.1021/bi801487x PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
Download full validation report
