Structural Insight into the Substrate Specificity of Phosphodiesterases - Phosphodiesterases as Drug Targets - page 123

PDEs (Conti and Beavo 2007 ; Lugnier 2006 ). This chapter reviews the progress on
the understanding of structural features that contribute to determining the substrate
specificity of these enzymes.
2 The Active Site of PDEs
The first crystal structure of the PDE4B catalytic domain (Xu et al. 2000 ) and the
later structure of the PDE4D2 catalytic domain in complex with AMP (Huai et al.
2003 ) provide a full definition of the active sites of PDE families. The active sites of
PDEs can be divided into two major subpockets: a cN-binding subpocket and a
divalent metal-binding subpocket (Fig. 2 ). All the PDE families contain two
divalent metal ions that are essential for their catalytic functions. The first metal
was identified by X-ray anomalous scattering as zinc and coordinates with four
invariant residues (His164, His200, Asp201, and Asp318 in PDE4D2, Table 1 ) and
two water molecules in an octahedral configuration (Fig. 2b ). The second metal also
forms six co-ordinations with an aspartic acid (Asp201 in PDE4D2) and five waters
in an octahedral configuration, but its chemical nature is not clear. Magnesium has
been in general accepted as the second catalytic ion for all PDE families, although
early reports showed that other divalent metal ions such as manganese and cobalt
promote the catalytic activity as effectively as does magnesium (Hitchcock 1973 ).
Besides, manganese was shown to support twice the catalytic activity of PDE9 and
PDE8 as that supported by magnesium (Fisher et al. 1998 ; Huai et al. 2004 ; Wang
et al. 2008 ). Moreover, the affinity of PDE5 for manganese is 30-100-fold that for
magnesium, although maximum catalytic activity is similar for the two metal ions
Fig. 2 Active site pocket of PDE4D2 in complex with 5 0 -AMP. (a) The product (5 0 -AMP) binding
at the active site. The dotted lines represent hydrogen bonds or metal coordinations. (b) Each of
two divalent metal ions forms six coordinations ( dotted lines ) in octahedral conformation. The
small red balls are water molecules. The identity of the second metal has not been determined, but
is depicted here as magnesium