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PDBsum entry 2fgy
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References listed in PDB file
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Key reference
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Title
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The structure of beta-Carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two.
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Authors
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M.R.Sawaya,
G.C.Cannon,
S.Heinhorst,
S.Tanaka,
E.B.Williams,
T.O.Yeates,
C.A.Kerfeld.
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Ref.
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J Biol Chem, 2006,
281,
7546-7555.
[DOI no: ]
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PubMed id
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Abstract
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CsoSCA (formerly CsoS3) is a bacterial carbonic anhydrase localized in the shell
of a cellular microcompartment called the carboxysome, where it converts
HCO(3)(-) to CO(2) for use in carbon fixation by ribulose-bisphosphate
carboxylase/oxygenase (RuBisCO). CsoSCA lacks significant sequence similarity to
any of the four known classes of carbonic anhydrase (alpha, beta, gamma, or
delta), and so it was initially classified as belonging to a new class, epsilon.
The crystal structure of CsoSCA from Halothiobacillus neapolitanus reveals that
it is actually a representative member of a new subclass of beta-carbonic
anhydrases, distinguished by a lack of active site pairing. Whereas a typical
beta-carbonic anhydrase maintains a pair of active sites organized within a
two-fold symmetric homodimer or pair of fused, homologous domains, the two
domains in CsoSCA have diverged to the point that only one domain in the pair
retains a viable active site. We suggest that this defunct and somewhat
diminished domain has evolved a new function, specific to its carboxysomal
environment. Despite the level of sequence divergence that separates CsoSCA from
the other two subclasses of beta-carbonic anhydrases, there is a remarkable
level of structural similarity among active site regions, which suggests a
common catalytic mechanism for the interconversion of HCO(3)(-) and CO(2).
Crystal packing analysis suggests that CsoSCA exists within the carboxysome
shell either as a homodimer or as extended filaments.
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Figure 3.
FIGURE 3. The loss of active site pairing in carboxysomal
 -carbonic anhydrases. In
P. sativum (A, upper panel), active site pairing is accomplished
through homodimerization. Molecule A of the dimer is shown in
yellow; molecule B is shown in red. Green spheres mark the
location of the two identical active site zinc ions. An ellipse
marks the location of a two-fold symmetry axis. Superimposed
molecules A and B are shown in C, lower panel. Only the very
C-terminal (C-term) tails are not superimposable (colored gray).
In P. purpureum (B, upper panel), the same pairing is
accomplished by a single polypeptide, not a dimer. The
N-terminal (N-term) domain is shown in yellow; the C-terminal
domain is shown in red. Pseudo-two-fold symmetry is still
evident but is not exact (B, lower panel). Non-superimposable
regions are shown in gray. Presumably, the P. purpureum carbonic
anhydrase arose from gene duplication and fusion. Divergence
appears minimal (70% sequence identity between domains). In A,
upper panel, CsoSCA, like the P. purpureum enzyme appears to be
the result of gene duplication and fusion. However, divergence
between the two internal domains has progressed to the extent
that the C-terminal domain has lost all active site residues
that it presumably once contained. Superimposed catalytic and
C-terminal domains (C, lower panel) show much larger areas of
structural nonequivalence (gray).
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Figure 4.
FIGURE 4. Conservation of active site structure and
mechanism. A, currently available structures of -carbonic
anhydrases can be divided into two groups: those in which the
conserved aspartate and arginine residues are hydrogen-bonded to
each other (CsoSCA, P. sativum, M. thermoautotrophicum, and
Rv1284) and those in which the hydrogen bonds are broken (P.
purpureum, E. coli, and Rv3588c). These are represented in dark
gray and light gray, respectively. In the former group, a water
molecule serves as the fourth ligand to the zinc ion. In the
latter group, the aspartate plays this role. The duality of
conformations suggests a conformational flexibility that might
play a role in catalysis. Residue numbering corresponds to
CsoSCA. B, a stereo figure showing a superpositioning of CsoSCA
(light gray) and P. sativum (dark gray) enzymes. A  ion
was modeled into the active site, based on similarities with the
position of the acetate ion found in the P. sativum structure.
Small changes in orientation of the allowed
hydrogen bonds to form between the and
zinc, His-397, Asp-175, and backbone nitrogens of Ala-254 and
Ala-255.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
7546-7555)
copyright 2006.
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