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PDBsum entry 1dv2
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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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Movement of the biotin carboxylase b-Domain as a result of ATP binding.
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Authors
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J.B.Thoden,
C.Z.Blanchard,
H.M.Holden,
G.L.Waldrop.
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Ref.
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J Biol Chem, 2000,
275,
16183-16190.
[DOI no: ]
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PubMed id
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Abstract
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Acetyl-CoA carboxylase catalyzes the first committed step in fatty acid
synthesis. In Escherichia coli, the enzyme is composed of three distinct protein
components: biotin carboxylase, biotin carboxyl carrier protein, and
carboxyltransferase. The biotin carboxylase component has served for many years
as a paradigm for mechanistic studies devoted toward understanding more
complicated biotin-dependent carboxylases. The three-dimensional x-ray structure
of an unliganded form of E. coli biotin carboxylase was originally solved in
1994 to 2.4-A resolution. This study revealed the architecture of the enzyme and
demonstrated that the protein belongs to the ATP-grasp superfamily. Here we
describe the three-dimensional structure of the E. coli biotin carboxylase
complexed with ATP and determined to 2.5-A resolution. The major conformational
change that occurs upon nucleotide binding is a rotation of approximately 45(o)
of one domain relative to the other domains thereby closing off the active site
pocket. Key residues involved in binding the nucleotide to the protein include
Lys-116, His-236, and Glu-201. The backbone amide groups of Gly-165 and Gly-166
participate in hydrogen bonding interactions with the phosphoryl oxygens of the
nucleotide. A comparison of this closed form of biotin carboxylase with
carbamoyl-phosphate synthetase is presented.
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Figure 2.
Fig. 2. Mode of binding of the inorganic phosphate ion to
biotin carboxylase. Shown in a is a representative portion of
the electron density map near the phosphate. The map, contoured
at 1  , was
calculated with coefficients of the form (2F[o]  F[c]),
where F[o] was the native structure factor amplitude and F[c]
was the calculated structure factor amplitude. The hydrogen
bonding pattern around the phosphate ion is indicated by the
dashed lines in b. Water molecules are depicted as red spheres.
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Figure 5.
Fig. 5. Superposition of the  -carbon
trace of native biotin carboxylase onto that of the E288K
protein/ATP complex. The unliganded form of biotin carboxylase
is shown in red bonds, while the E288K protein is displayed in
black bonds. The ATP is depicted in a ball-and-stick
representation.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2000,
275,
16183-16190)
copyright 2000.
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