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PDBsum entry 3bob
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References listed in PDB file
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Key reference
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Title
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Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms.
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Authors
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Y.Xu,
L.Feng,
P.D.Jeffrey,
Y.Shi,
F.M.Morel.
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Ref.
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Nature, 2008,
452,
56-61.
[DOI no: ]
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PubMed id
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Abstract
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Carbonic anhydrase, a zinc enzyme found in organisms from all kingdoms,
catalyses the reversible hydration of carbon dioxide and is used for inorganic
carbon acquisition by phytoplankton. In the oceans, where zinc is nearly
depleted, diatoms use cadmium as a catalytic metal atom in cadmium carbonic
anhydrase (CDCA). Here we report the crystal structures of CDCA in four distinct
forms: cadmium-bound, zinc-bound, metal-free and acetate-bound. Despite lack of
sequence homology, CDCA is a structural mimic of a functional beta-carbonic
anhydrase dimer, with striking similarity in the spatial organization of the
active site residues. CDCA readily exchanges cadmium and zinc at its active
site--an apparently unique adaptation to oceanic life that is explained by a
stable opening of the metal coordinating site in the absence of metal. Given the
central role of diatoms in exporting carbon to the deep sea, their use of
cadmium in an enzyme critical for carbon acquisition establishes a remarkable
link between the global cycles of cadmium and carbon.
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Figure 1.
Figure 1: Structure of the second CA repeat of CDCA1 (CDCA1-R2).
a, Overall structure of the Cd-bound CDCA1-R2. Two lobes of
the structure are coloured blue and green. Cd is highlighted in
red, and Cd-coordinating residues are coloured yellow. b,
Comparison of the active site conformation between CDCA-R2
(green) and 
-CA (blue). The active site residues in CDCA-R2 and -CA
are coloured yellow and orange, respectively. Hydrogen bonds are
represented by red dashed lines. Cd and the water ligand are
shown in large and small red spheres, respectively. (A stereo
view is shown in Supplementary Fig. 1b.) c, Comparison of Cd-
and Zn-coordination in CDCA1-R2. Metal coordination and hydrogen
bonds are indicated by red and green dashed lines, respectively;
numbers indicate bond lengths in Å. W1–W3, water
molecules. Structural images were prepared using MOLSCRIPT^44
and GRASP^45.
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Figure 3.
Figure 3: Structure of CDCA1-R2 bound to substrate analogue
acetate. a, A close-up view of the region around acetate. The
F[o] - F[c] electron density map surrounding acetate was
calculated using simulated annealing with the omission of
acetate and was contoured at 5  .
b, A close-up view of the active site conformation. Metal
coordination and hydrogen bonds are indicated by red and green
dashed lines, respectively. Relevant distances are indicated
(Å). c, A hydrophobic channel traverses through CDCA1-R2.
Cd is highlighted in red. Acetate is shown in yellow. The
conserved hydrophobic residues that line the channel are shown
in magenta. (Stereo views of a and b are shown in Supplementary
Fig.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2008,
452,
56-61)
copyright 2008.
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