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PDBsum entry 2a00
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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 holo-Form of the nucleotide binding domain of the kdpfabc complex from escherichia coli reveals a new binding mode.
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Authors
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M.Haupt,
M.Bramkamp,
M.Heller,
M.Coles,
G.Deckers-Hebestreit,
B.Herkenhoff-Hesselmann,
K.Altendorf,
H.Kessler.
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Ref.
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J Biol Chem, 2006,
281,
9641-9649.
[DOI no: ]
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PubMed id
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Abstract
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P-type ATPases are ubiquitously abundant enzymes involved in active transport of
charged residues across biological membranes. The KdpB subunit of the
prokaryotic Kdp-ATPase (KdpFABC complex) shares characteristic regions of
homology with class II-IV P-type ATPases and has been shown previously to be
misgrouped as a class IA P-type ATPase. Here, we present the NMR structure of
the AMP-PNP-bound nucleotide binding domain KdpBN of the Escherichia coli
Kdp-ATPase at high resolution. The aromatic moiety of the nucleotide is clipped
into the binding pocket by Phe(377) and Lys(395) via a pi-pi stacking and a
cation-pi interaction, respectively. Charged residues at the outer rim of the
binding pocket (Arg(317), Arg(382), Asp(399), and Glu(348)) stabilize and direct
the triphosphate group via electrostatic attraction and repulsion toward the
phosphorylation domain. The nucleotide binding mode was corroborated by the
replacement of critical residues. The conservative mutation F377Y produced a
high residual nucleotide binding capacity, whereas replacement by alanine
resulted in low nucleotide binding capacities and a considerable loss of ATPase
activity. Similarly, mutation K395A resulted in loss of ATPase activity and
nucleotide binding affinity, even though the protein was properly folded. We
present a schematic model of the nucleotide binding mode that allows for both
high selectivity and a low nucleotide binding constant, necessary for the fast
and effective turnover rate realized in the reaction cycle of the Kdp-ATPase.
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Figure 7.
FIGURE 7. Zoom into the nucleotide binding pocket. The
stereo view of the binding pocket backs the critical role of
Phe^377 and Lys^395 for nucleotide binding, depicted are all
residues that are within a sphere of 10 Å around the
nucleotide.
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Figure 8.
FIGURE 8. Clip to fit. The schematic picture of the
nucleotide binding pocket illustrates the simple and
energy-saving nucleotide binding mode, enabling the rapid
nucleotide exchange necessary for a functional reaction cycle.
Highlighted are the residues Phe^377, Lys^395, Arg^317, and
Arg^382. Asp^344 is represented as a negative charge at the
bottom of the binding pocket by a red circle.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
9641-9649)
copyright 2006.
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