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DOI no:
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J Biol Chem
283:19657-19664
(2008)
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PubMed id:
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Crystal structure of the GAF-B domain from human phosphodiesterase 10A complexed with its ligand, cAMP.
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N.Handa,
E.Mizohata,
S.Kishishita,
M.Toyama,
S.Morita,
T.Uchikubo-Kamo,
R.Akasaka,
K.Omori,
J.Kotera,
T.Terada,
M.Shirouzu,
S.Yokoyama.
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ABSTRACT
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Cyclic nucleotide phosphodiesterases (PDEs) catalyze the degradation of the
cyclic nucleotides cAMP and cGMP, which are important second messengers. Five of
the 11 mammalian PDE families have tandem GAF domains at their N termini. PDE10A
may be the only mammalian PDE for which cAMP is the GAF domain ligand, and it
may be allosterically stimulated by cAMP. PDE10A is highly expressed in striatal
medium spiny neurons. Here we report the crystal structure of the C-terminal GAF
domain (GAF-B) of human PDE10A complexed with cAMP at 2.1-angstroms resolution.
The conformation of the PDE10A GAF-B domain monomer closely resembles those of
the GAF domains of PDE2A and the cyanobacterium Anabaena cyaB2 adenylyl cyclase,
except for the helical bundle consisting of alpha1, alpha2, and alpha5. The
PDE10A GAF-B domain forms a dimer in the crystal and in solution. The
dimerization is mainly mediated by hydrophobic interactions between the helical
bundles in a parallel arrangement, with a large buried surface area. In the
PDE10A GAF-B domain, cAMP tightly binds to a cNMP-binding pocket. The residues
in the alpha3 and alpha4 helices, the beta6 strand, the loop between 3(10) and
alpha4, and the loop between alpha4 and beta5 are involved in the recognition of
the phosphate and ribose moieties. This recognition mode is similar to those of
the GAF domains of PDE2A and cyaB2. In contrast, the adenine base is
specifically recognized by the PDE10A GAF-B domain in a unique manner, through
residues in the beta1 and beta2 strands.
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Selected figure(s)
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Figure 3.
FIGURE 3. Recognition of cAMP by the GAF-B domain of
PDE10A. A, a semi-transparent surface representation, viewed
from the opening of the cAMP-binding pocket. The bound cAMP
molecule is represented by a yellow ball-and-stick model, with
oxygen, nitrogen, and phosphorus atoms shown in red, blue, and
purple, respectively. A simulated annealing omit  [calc](|F[o]| - |F[c]|)
map was calculated without the cAMP molecule atoms to
2.1-Å resolution, and was contoured at 3.0  . B,
stereo diagram showing the cAMP recognition. The bound cAMP
(yellow) and the interacting residues (white) are shown by
ball-and-stick models, with oxygen, nitrogen, phosphorus, and
sulfur atoms shown in red, blue, purple, and orange,
respectively. Two water molecules are shown as red spheres. In
the ribbon model, the β strands are cyan, the helices
are salmon, the 3[10] helix is green, and the random coils are
gray. Hydrogen bonds between cAMP and the protein are indicated
by broken red lines.
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Figure 4.
FIGURE 4. cNMP recognition by GAF domains. Hydrogen bonds
are indicated by broken red lines. A, stereo diagram showing the
superposition of GAF domains complexed with cNMP from PDE10A,
PDE2A, and cyaB2. The GAF domains except for the helical bundles
are represented by gray tube models. The cNMP molecules are
represented by blue stick models. Amino acid side chains at
positions equivalent to Phe^304 (PDE2A, Phe^438; cyaB2,
Ile^308), Val^356 (PDE2A, Val^484; cyaB2, Ile^355), Asp^357
(PDE2A, Asp^485; cyaB2, Asp^356), Thr^360 (PDE2A, Thr^488;
cyaB2, Thr^172/Asn^359), Thr^364 (PDE2A, Thr^492; cyaB2,
Thr^176/Thr^363), Gln^383 (PDE2A, Glu^512; cyaB2,
Gln^196/Gln^383), Val^385 (PDE2A, Val^514; cyaB2,
Leu^198/Val^385), in PDE10A are shown, and backbone atoms at
positions equivalent to Ile^330 (PDE2A, Ile^458; cyaB2,
Ile^139/Phe^326) and Ala^331 (PDE2A, Ala^459; cyaB2,
Ala^140/Ala^327) are shown. Residues making hydrophobic
interactions with cNMP are orange, residues making hydrogen
bonds to the O2' are sky blue, residues making water-mediated
hydrogen bonds to bases are pink, and residues making hydrogen
bonds to phosphate groups are green. One water molecule is
shown, as a red sphere. B, stereo diagram showing the
superimposed ball-and-stick models of the bases and the residues
making direct hydrogen bonds to the bases. Residues in the
PDE10A GAF-B domain complexed with cAMP are green, residues in
the PDE2A GAF-B domain complexed with cGMP are magenta, residues
in the cyaB2 GAF-A domain complexed with cAMP are yellow, and
residues in the cyaB2 GAF-B domain complexed with cAMP are
orange. Oxygen, nitrogen, and sulfur atoms are red, blue, and
orange, respectively.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2008,
283,
19657-19664)
copyright 2008.
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Figures were
selected
by an automated process.
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177 a.a.
