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5 0 -nucleotide product or the selective inhibitors are now available (Ke and Wang
2007b ; Wang et al. 2007 ; Xu et al. 2000 , 2004 ). Interestingly, the orientation of
substrate, inhibitor, or product can vary substantially among PDEs (Wang, Liu, Hou
2007 ). This may be due to the relatively large volume of the catalytic site compared
to the size of the substrate/product or most inhibitors. However, this variation
restricts the potential for generalizations from one structure to another. Recently,
X-ray crystal structures of two PDEs containing either the near-full length regu-
latory domain (PDE2) (Pandit et al. 2009 ) or a portion thereof (PDE4) (Burgin et al.
2010 ) have been published. Both structures provide important new insights into
regulatory domain functions, and the report on the PDE4 constructs reveals novel
new approaches to inhibitor design and action (see below and in Gurney et al. in
Chapter 7 in this volume). However, the X-ray crystal structure of PDE2 defines the
structure in the absence of cGMP, that is, the lower activity state of the enzyme, and
provides only a partial picture of the functional states of PDE2 (Pandit et al. 2009 ).
In X-ray crystal structures of isolated catalytic domains in complex with various
inhibitors, substrates, or catalytic products, hydrogen bonding with an invariant
glutamine and hydrophobic stacking of the ring structure of the substrate/product/
inhibitor with a conserved phenylalanine (in most PDEs) are common interactions
(Fig. 2 ) (Ke and Wang 2007a , b ; Xu et al. 2000 , 2004 ). Another group of amino
acids in the catalytic pocket forms a hydrophobic face that wedges the ring structure
of the ligands against the conserved phenylalanine, thereby creating what has been
termed a “hydrophobic clamp.” These interactions occur for most PDEs when
associated with a wide spectrum of inhibitors/products that vary significantly in
affinities and chemical characteristics (Ke and Wang 2007b ).
For several PDE holoenzymes, the energy contribution of amino acids in the
catalytic pockets to the affinity for substrate or inhibitors have been quantified using
site-directed mutagenesis (Burgin et al. 2010 ; Cheung et al. 1998 ; Jacobitz et al.
1996 ; Jin et al. 1992 ; Omburo et al. 1998 ; Turko et al. 1999 ; Wang et al. 2005 ;
Zhang et al. 2002 ; Zoraghi et al. 2007 ). It is evident from the X-ray crystallography
and mutagenesis studies that different inhibitors exploit novel features in and near
the catalytic sites of the respective PDEs to enhance potency and selectivity (Ke and
Wang 2007b ; Sung et al. 2003 ; Wu et al. 2004 ). In some instances, enhanced
specificity/potency is provided by sequence(s) well outside the catalytic domain
(Blount et al. 2006 ; Burgin et al. 2010 ; McPhee et al. 1999 ; Omori and Kotera 2006 ;
Richter and Conti 2004 ; Saldou et al. 1998 ), but currently insights into the mechan-
isms that provide for this are limited.
1.4 Functional Distinctions Among PDE Catalytic Sites
1.4.1 Catalytic Characteristics
Despite strong structural similarities among the PDE catalytic sites, PDEs 4, 7, and
8 are highly specific for hydrolysis of cAMP, PDEs 5, 6, and 9 are highly specific
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