PDBsum entry 3ecm

Hydrolase

PDB id: 3ecm

Contents

Protein chain

338 a.a. *

Metals

_MG

_ZN

Waters ×68

* Residue conservation analysis

PDB id:

3ecm

Name:

Hydrolase

Title:

Crystal structure of the unliganded pde8a catalytic domain

Structure:

High affinity camp-specific and ibmx-insensitive 3',5'- cyclic phosphodiesterase 8a. Chain: a. Fragment: the catalytic domain of pde8a1 (unp residues 482-819). Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pde8a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.236 R-free: 0.265

Authors:

H.Wang,Z.Yan,S.Yang,J.Cai,H.Robinson,H.Ke

Key ref:

H.Wang et al. (2008). Kinetic and structural studies of phosphodiesterase-8A and implication on the inhibitor selectivity. Biochemistry, 47, 12760-12768. PubMed id: 18983167

Date:

01-Sep-08 Release date: 25-Nov-08

Protein chain

O60658  (PDE8A_HUMAN) -  High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A from Homo sapiens

Seq: 829 a.a.

Struc: 338 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.4.53 - 3',5'-cyclic-AMP phosphodiesterase.
• Reaction: 3',5'-cyclic AMP + H2O = AMP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Biochemistry 47:12760-12768 (2008)

PubMed id: 18983167

Kinetic and structural studies of phosphodiesterase-8A and implication on the inhibitor selectivity.

H.Wang, Z.Yan, S.Yang, J.Cai, H.Robinson, H.Ke.

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.