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PDBsum entry 1k3c
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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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The phosphoryl-Transfer mechanism of escherichia coli phosphoenolpyruvate carboxykinase from the use of alf(3).
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Authors
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A.M.Sudom,
L.Prasad,
H.Goldie,
L.T.Delbaere.
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Ref.
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J Mol Biol, 2001,
314,
83-92.
[DOI no: ]
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PubMed id
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Abstract
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The mechanism of reversible transfer of the gamma-phosphate group of ATP by
Escherichia coli phosphoenolpyruvate carboxykinase (PCK) on to its substrate is
of great interest. It is known that metallofluorides are accurate analogs of the
transition state in the context of kinase mechanisms. Therefore, two complexes
of PCK, one with AlF(3), Mg(2+) and ADP (complex I), the other with AlF(3),
Mg(2+), ADP and pyruvate (complex II) were crystallized. The X-ray crystal
structures of these two complexes were determined at 2.0 A resolution. The Al
atom has trigonal bipyramidal geometry that mimics the transition state of
phosphoryl transfer. The Al atom is at a distance of 2.8 A and 2.9 A from an
oxygen atom of the beta-phosphoryl group of ADP in complex I and II,
respectively. A water molecule in complex I and an oxygen atom of the pyruvate
in complex II are located along the axis of the trigonal bipyramid on the side
opposite to the beta-phosphoryl oxygen with respect to the equatorial plane,
suggesting that the complexes are close mimics of the transition state. Along
with the presence of positively charged species around the AlF(3) moiety, these
results indicate that phosphoryl transfer occurs via a direct displacement
mechanism with associative qualities.
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Figure 1.
Figure 1. The associative (SN2-like) versus dissociative
(SN1-like) mechanisms of phosphoryl transfer. As can be seen in
the associative state, one bond is formed between the incoming
nucleophile and attacked phosphorus atom concurrently with the
existing bond between Pg and the b, g-bridging oxygen. The
dissociative state first involves bond breaking between Pg and
the b, g-bridging oxygen, then bond formation occurs. The two
states also differ in geometry and charge distribution, as the
associative case involves a pentagonal bipyramidal structure (
-3) and the dissociative case involves a planar, trigonal
phosphorane ( -1).
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Figure 4.
Figure 4. Detailed diagram illustrating AlF[3] binding in
the active site region of the ADP-Mg2+-AlF[3] E. coli PCK
quaternary complex. Note that the fluorine atoms interact
primarily with basic residues or Mg2+. The aluminum atom is
close to an oxygen atom of the b-phosphoryl group of ATP. Mg2+
is the light blue sphere, the aluminum atom is colored pink, the
fluorine atoms are colored green. (a) PCK-ADP-AlF[3]-Mg2+
complex (complex I). (b) PCK-ADP-AlF[3]-Mg2+-pyruvate complex
(complex II).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
314,
83-92)
copyright 2001.
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