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PDBsum entry 3itm
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References listed in PDB file
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Key reference
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Title
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Mechanism for the allosteric regulation of phosphodiesterase 2a deduced from the X-Ray structure of a near full-Length construct.
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Authors
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J.Pandit,
M.D.Forman,
K.F.Fennell,
K.S.Dillman,
F.S.Menniti.
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Ref.
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Proc Natl Acad Sci U S A, 2009,
106,
18225-18230.
[DOI no: ]
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PubMed id
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Abstract
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We report the X-ray crystal structure of a phosphodiesterase (PDE) that includes
both catalytic and regulatory domains. PDE2A (215-900) crystallized as a dimer
in which each subunit had an extended organization of regulatory GAF-A and GAF-B
and catalytic domains connected by long alpha-helices. The subunits cross at the
GAF-B/catalytic domain linker, and each side of the dimer contains in series the
GAF-A and GAF-B of one subunit and the catalytic domain of the other subunit. A
dimer interface extends over the entire length of the molecule. The substrate
binding pocket of each catalytic domain is occluded by the H-loop. We deduced
from comparisons with structures of isolated, ligand-bound catalytic subunits
that the H-loop swings out to allow substrate access. However, in dimeric PDE2A
(215-900), the H-loops of the two catalytic subunits pack against each other at
the dimer interface, necessitating movement of the catalytic subunits to allow
for H-loop movement. Comparison of the unliganded GAF-B of PDE2A (215-900) with
previous structures of isolated, cGMP-bound GAF domains indicates that cGMP
binding induces a significant shift in the GAF-B/catalytic domain linker. We
propose that cGMP binding to GAF-B causes movement, through this linker region,
of the catalytic domains, such that the H-loops no longer pack at the dimer
interface and are, instead, free to swing out to allow substrate access. This
increase in substrate access is proposed as the basis for PDE2A activation by
cGMP and may be a general mechanism for regulation of all PDEs.
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Figure 1.
Structure of hPDE2A (215–900). The asymmetric unit contains
two molecules, A and B, related by a noncrystallographic 2-fold
axis of symmetry, which, in this view, is roughly parallel to
the plane of the paper in the vertical direction. The three
domains are labeled in the figure, as well as the linker helices
LH1 and LH2 that connect them. Molecule B is shown in surface
representation, and molecule A is shown in a ribbons
representation, with the ribbons colored by crystallographic
B-factor, blue being low and red being high. Regions of the
structure with higher B-factors, such as the linker between the
GAF-B domain and the catalytic domain, are expected to be more
flexible. All side chains from molecule A that are within 3.5
Å of molecule B are shown as magenta sticks, The dimer
interface extends over the surface of the entire molecule. The
two catalytic sites in the vicinity of the Zn^2+ and Mg^2+ ions
(shown as gray and green spheres) mutually occlude each other at
the dimer interface. All figures showing the structure were
generated with PyMOL (www.pymol.org).
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Figure 3.
The two catalytic sites mutually occlude each other at the
dimer interface. (A) The catalytic domain of a single subunit of
the PDE2A (215–900) dimer is shown in ribbons representation,
with the H-loop colored in magenta and the M-loop colored in
blue. The active site, whose location can be inferred from the
position of the Zn^2+ and Mg^2+ ions (shown as gray and green
spheres) is partially occupied by residues from the H-loop.
Residues 840–850 of the M-loop have not been modeled due to
disorder and are indicated by a dotted line. (B) The second
subunit is shown as a semitransparent gray surface, as well as
in ribbons representation, keeping exactly the same orientation
as in panel A. The H-loop is blocked from swinging out of the
active site by the dimer interface.
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