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PDBsum entry 1geh
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a novel-Type archaeal rubisco with pentagonal symmetry.
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Authors
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K.Kitano,
N.Maeda,
T.Fukui,
H.Atomi,
T.Imanaka,
K.Miki.
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Ref.
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Structure, 2001,
9,
473-481.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key
enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2
fixation in plants, algae, and bacteria. Rubiscos have been so far classified
into two types. Type I is composed of eight large subunits (L subunits) and
eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II
is usually composed only of two L subunits (L2). Recently, some genuinely active
Rubiscos of unknown physiological function have been reported from archaea.
RESULTS: The crystal structure of Rubisco from the hyperthermophilic archaeon
Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 A resolution.
The enzyme is composed only of L subunits and showed a novel (L2)5 decameric
structure. Compared to previously known type I enzymes, each L2 dimer is
inclined approximately 16 degrees to form a toroid-shaped decamer with its
unique L2-L2 interfaces. Differential scanning calorimetry (DSC), circular
dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco
maintains its secondary structure and decameric assembly even at high
temperatures. CONCLUSIONS: The present study provides the first structure of an
archaeal Rubisco, an unprecedented (L2)5 decamer. Biochemical studies indicate
that Tk-Rubisco maintains its decameric structure at high temperatures. The
structure is distinct from type I and type II Rubiscos and strongly supports
that Tk-Rubisco should be classified as a novel type III Rubisco.
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Figure 4.
Figure 4. Oligomeric Structures of Rubiscos(a) Decamer
structure of Tk-Rubisco, with ribbon diagram from top view. Each
monomer is shown in different colors and labeled from "A" to
"J." Plausible structures of RuBP molecules and magnesium ions
are marked in ellipses.(b) Side view of Tk-Rubisco by -90°
rotation from (a), with the AB dimer at the center.(c) The
(L[2])[4] core of type I Rubisco, with ribbon diagram from top
view, where only L subunits in the L[8]S[8] structure [11] are
shown. Each monomer is shown in different colors. RuBP molecules
and magnesium ions are marked in ellipses.(d) Side view of the
(L[2])[4] core of type I Rubisco by -90° rotation from (c)
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2001,
9,
473-481)
copyright 2001.
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Secondary reference #1
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Title
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Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon pyrococcus kodakaraensis kod1 is composed solely of large subunits and forms a pentagonal structure.
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Authors
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N.Maeda,
K.Kitano,
T.Fukui,
S.Ezaki,
H.Atomi,
K.Miki,
T.Imanaka.
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Ref.
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J Mol Biol, 1999,
293,
57-66.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Crystals of recombinant Pk-Rubisco by the hanging
drop vapor diffusion. The bar indicates 0.5 mm.
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Figure 5.
Figure 5. X-ray diffraction photograph of recombinant
Pk-Rubisco crystals. The diffraction was taken by the
Weissenberg method with synchrotron radiation at PF-BL6B, KEK,
Japan. Rotation range is 5.3 ° and the crystal-to-film
distance is 573 mm. The arrow indicates diffraction at 3.0
Å resolution.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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