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PDBsum entry 2qw7
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Structural protein
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PDB id
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2qw7
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References listed in PDB file
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Key reference
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Title
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Atomic-Level models of the bacterial carboxysome shell.
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Authors
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S.Tanaka,
C.A.Kerfeld,
M.R.Sawaya,
F.Cai,
S.Heinhorst,
G.C.Cannon,
T.O.Yeates.
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Ref.
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Science, 2008,
319,
1083-1086.
[DOI no: ]
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PubMed id
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Abstract
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The carboxysome is a bacterial microcompartment that functions as a simple
organelle by sequestering enzymes involved in carbon fixation. The carboxysome
shell is roughly 800 to 1400 angstroms in diameter and is assembled from several
thousand protein subunits. Previous studies have revealed the three-dimensional
structures of hexameric carboxysome shell proteins, which self-assemble into
molecular layers that most likely constitute the facets of the polyhedral shell.
Here, we report the three-dimensional structures of two proteins of previously
unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of
carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble
to form pentameric structures whose size and shape are compatible with formation
of vertices in an icosahedral shell. Combining these pentamers with the hexamers
previously elucidated gives two plausible, preliminary atomic models for the
carboxysome shell.
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Figure 2.
Fig. 2. Crystal structures of the carboxysome proteins CcmL and
OrfA revealing pentagonal symmetry. (A) Structure of the CcmL
monomer from Syn. 6803. (B) A comparison of similar structures:
CcmL (blue), OrfA (or CsoS4A) from H. neapolitanus (yellow), and
EutN from E. coli (pink) (PDB 2Z9H). The RMSD between the
protein backbones of CcmL and OrfA is 1.0 Å, and 1.3
Å between CcmL and EutN. (C) CcmL and OrfA assemble as
natural pentamers. EutN, which is part of the eut operon that
encodes proteins presumed to comprise the distinct eut
microcompartment in E. coli, is instead hexameric. (D) Top and
side views of the CcmL pentamer showing a pentagonal disk with
slanted sides.
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Figure 3.
Fig. 3. Models of the carboxysome shell based on pentamer and
hexamer components. (A) A flat layer of hexagons can be folded
to give pentagonal vertices by removing one sector at each
vertex. Twelve such vertices are present in an icosahedral
shell. (B) Taken in combination, alternate choices for the
curvature of the hexagonal layer and the orientation of the
pentamer lead to four possible constructions, numbered 1 to 4
according to the quality of fit. Combination 4 led to impossible
steric collisions. The structures are colored according to
calculated electrostatic potential, from negative (red) to
positive (blue). (C) Illustration of the best packing solutions
for constructions 1 to 3. EN, calculated packing energies (27)
(with more negative values being favorable); SC, surface
complementarity (26); and SA, buried surface area between a
pentamer and a single neighboring hexamer (with higher values of
these parameters being favorable). (D) Two alternate models for
the complete carboxysome shell, based on the two constructions,
1 and 2, judged to be most plausible. There are 740 hexamers and
12 pentamers in a T = 75 arrangement. The packing of hexamers is
derived from multiple consistent crystal structures. The two
models differ with respect to the orientation of the hexameric
layer. The hexagonal layer is colored according to
hydrophobicity, with increases showing as blue to orange. The
CcmL pentamers are shown in magenta. The diameter from vertex to
vertex is 1150 Å.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2008,
319,
1083-1086)
copyright 2008.
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