Biology Reference
In-Depth Information
among mammalian PDEs and comprises ~270 amino acids (Bender and Beavo
2006
;
Conti and Beavo
2007
), is located toward the carboxyl-terminal portion of the
PDEs and exhibits 24-51% amino acid sequence identity among the 11 families.
X-ray crystal structures of the isolated catalytic domains have shown that the
various PDEs share a similar overall topography that is comprised almost entirely
of
a
-helices (16-17 helices), as well as sharing common structural features in the
composition and conformation of the catalytic pockets (Ke and Wang
2007b
;
Zhang
2006
). However, there are important differences among these proteins in
the binding of cNs and inhibitors (Wang et al.
2005
; Wang, Liu, Hou et al. 2007;
Wang, Yan, Yang, Cai et al. 2008; Huai, Wang, Zhang et al. PNAS 2004; Huai, Liu,
Francis, Corbin JBC 2004). Moreover, potent and selective inhibitors of PDE4 have
recently been developed by dually targeting the catalytic sites of these enzymes
together with regions outside the catalytic pocket itself (Burgin et al.
2010
; Gurney
et al.
2011
).
1.3 Structural Characteristics
Divalent metal ions are required for catalytic function of all PDEs. In the X-ray
crystallographic structures of PDEs, the catalytic pockets have been shown to
contain a novel binuclear metal-binding site that is thought to contribute critical
elements of the catalytic mechanism (Xu et al.
2000
). Where it has been studied, the
interactions of certain inhibitors with PDE catalytic sites can be influenced by the
presence of these metal ions, but direct or indirect interaction with the metals does
not appear to substantially impact potency (Chen et al.
2008
; Corbin et al.
2003
;Ke
and Wang
2007b
; Sung et al.
2003
; Wang et al.
2008
). However, it is reasonable
that inhibitors could be designed that utilize contacts with one or more of the metal
ions or that expel these cofactors, thereby eliminating catalytic activity. Since
affinity of certain PDE4 long isoforms for various selective inhibitors and magne-
sium is sensitive to PKA phosphorylation of the regulatory UCR1 domain (Alvarez
et al.
1995
; Sette and Conti
1996
b; Hoffmann et al.
1998
), it seems likely that the
metal ions bound to a particular PDE could also affect its interaction with certain
inhibitors. Moreover, some inhibitors could influence metal occupancy of PDE
catalytic sites (Wang et al.
2008
), but this possibility has not yet been investigated.
Results of X-ray crystallographic studies of certain PDEs reveal that a hydroxyl
derived from solvent water bridges the two metal ions in these catalytic sites. This
arrangement provides for production of a highly nucleophilic hydroxyl that inserts
at the phosphate in the cyclic phosphate ring of the cN and breaks the ring (Fig.
2
)
(Liu et al.
2008
). These data are consistent with the results of early biochemical
studies establishing that the hydroxyl inserted into the cyclic phosphate ring is
derived from solvent water and that the stereochemistry of the product is consistent
with this mechanism (Braumann et al.
1986
; Burgers and Eckstein
1979
; Jarvest
et al.
1982
; Walseth et al.
1983
). In most instances, one of the metal sites is occupied
by a zinc that is very tightly bound, and the other site is occupied by a more loosely
