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PDBsum entry 1wc0
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References listed in PDB file
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Key reference
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Title
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Bicarbonate activation of adenylyl cyclase via promotion of catalytic active site closure and metal recruitment.
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Authors
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C.Steegborn,
T.N.Litvin,
L.R.Levin,
J.Buck,
H.Wu.
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Ref.
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Nat Struct Mol Biol, 2005,
12,
32-37.
[DOI no: ]
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PubMed id
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Abstract
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In an evolutionarily conserved signaling pathway, 'soluble' adenylyl cyclases
(sACs) synthesize the ubiquitous second messenger cyclic adenosine
3',5'-monophosphate (cAMP) in response to bicarbonate and calcium signals. Here,
we present crystal structures of a cyanobacterial sAC enzyme in complex with ATP
analogs, calcium and bicarbonate, which represent distinct catalytic states of
the enzyme. The structures reveal that calcium occupies the first ion-binding
site and directly mediates nucleotide binding. The single ion-occupied,
nucleotide-bound state defines a novel, open adenylyl cyclase state. In
contrast, bicarbonate increases the catalytic rate by inducing marked active
site closure and recruiting a second, catalytic ion. The phosphates of the bound
substrate analogs are rearranged, which would facilitate product formation and
release. The mechanisms of calcium and bicarbonate sensing define a reaction
pathway involving active site closure and metal recruitment that may be
universal for class III cyclases.
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Figure 3.
Figure 3. Conformational states and comparison of AC enzymes.
(a) Structure-based sequence alignment of bicarbonate responsive
sAC enzymes and the G protein -regulated tmAC domains VC[1] and
IIC[2] (PDB entry 1AZS). Secondary structure elements of sAC and
IIC[2] are indicated on top and bottom, respectively.
Ion-binding residues (  )
and residues binding the substrate (^) or the transition state (
 )
are labeled (filled and empty symbols label C[1] and C[2]
residues, respectively). Thr1139^* and the insertion
characteristic for sAC enzymes are indicated (  ).
Conserved amino acids are shaded yellow, and residues with
conserved physicochemical properties are shaded red. (b) Overlay
of the sAC -  ,
 -Me-ATP
structure (open state, darkest gray, with 1
helix and 7
- 8
loop in blue), the sAC -Rp-ATP S
complex (partially closed, middle gray and red), and the
bicarbonate-soaked Rp-ATP S
structure (closed, lightest gray and yellow). Structures were
superimposed on sAC - ,
-Me-ATP
by optimizing positional agreement for residues 1014 -1018, 1056
-1065, 1117 -1126 and 1143 -1167 in both subunits. (c) sAC
active site in complex with Rp-ATP S
and two magnesium ions, with the two monomers colored red and
blue, respectively. The dashed lines indicate the octahedral
coordination of the ions through the ATP analog, protein
residues and one and two water molecules (gold spheres),
respectively. The 2F[o] - F[c] omit electron density for the
ligands was contoured at 1.1  .
In its tmAC complex, P of
Rp-ATP S
was modeled differently but with limited electron density for
the ribose and its link to the P 16,
and we speculate that this density might also be interpretable
with the inhibitor conformation observed here for its sAC
complex.
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Figure 4.
Figure 4. Model for catalysis by class III nucleotidyl cyclases.
The model for catalysis (bottom pathway) is based on the
conformational changes observed with the sAC -substrate analog
complexes (top). The arrows at 1
and 7
- 8
indicate the movements undergone by these protein parts. The
individual catalytic states (open, intermediate and closed) are
extrapolated from the different sAC structures presented in the
text, with the protein conformation of the sAC -Rp-ATP S
complex being a speculative approximate intermediate state.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2005,
12,
32-37)
copyright 2005.
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