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PDBsum entry 1nhh
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Replication, signaling protein
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PDB id
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1nhh
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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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Monovalent cation dependence and preference of ghkl atpases and kinases.
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Authors
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X.Hu,
M.Machius,
W.Yang.
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Ref.
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FEBS Lett, 2003,
544,
268-273.
[DOI no: ]
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PubMed id
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Abstract
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The GHKL phosphotransferase superfamily, characterized by four sequence motifs
that form the ATP-binding site, consists of the ATPase domains of type II DNA
topoisomerases, Hsp90, and MutL, and bacterial and mitochondrial protein
kinases. In addition to a magnesium ion, which is essential for catalysis, a
potassium ion bound adjacent to the triphosphate moiety of ATP in a rat
mitochondrial protein kinase, BCK (branched-chain alpha-ketoacid dehydrogenase
kinase), has been shown to be indispensable for nucleotide binding and
hydrolysis. Using X-ray crystallographic, biochemical, and genetic analyses, we
find that the monovalent cation-binding site is conserved in MutL, but both
Na(+) and K(+) support the MutL ATPase activity. When Ala100 of MutL is
substituted by proline, mimicking the K(+)-binding environment in BCK, the
mutant MutL protein becomes exclusively dependent on Na(+) for the ATPase
activity. The coordination of this Na(+) ion is identical to that of the K(+)
ion in BCK and involves four carbonyl oxygen atoms emanating from the hinges of
the ATP lid and a non-bridging oxygen of the bound nucleotide. A similar
monovalent cation-binding site is found in DNA gyrase with additional
coordination by a serine side chain. The conserved and protein-specific
monovalent cation-binding site is unique to the GHKL superfamily and probably
essential for both ATPase and kinase activity. Dependence on different
monovalent cations for catalysis may be exploited for future drug design
specifically targeting each individual member of the GHKL superfamily.
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Figure 2.
Fig. 2. Crystal structures of the ATP-binding site of the
WT LN40, BCK and LN40(A100P). a: The active site configuration
of the LN40–ADPnP complex in the presence of Mg^2+ and K^+.
Peaks above 3σ in an anomalous difference Fourier map are
contoured in light blue. b: The ATPγS bound BCK. c: The active
site configuration of the LN40(A100P)–ADPnP complex. The ATP
analogs (ADPnP and ATPγS) are shown in yellow bonds, the
protein carbonyl groups in gray bonds, the Mg^2+ ion is shown in
dark green, Na^+ ion in light blue, and K^+ ion dark purple.
Coordination of the monovalent cation is highlighted in dark
pink.
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Figure 3.
Fig. 3. Comparison of the monovalent ion-binding site of
BCK, MutL, GyrB, human Hsp90 and CheA. Secondary structures
surrounding the ATP-binding site are shown in gray ribbon
drawings including motifs I (N) and IV; motif II (G1) and the N-
and C-terminal (motif III) hinges of ATP lid are drawn in
yellow. For clarity, the connecting part of the ATP lid is not
shown. The bound nucleotides are shown in ball-and-stick models,
divalent and monovalent cations are shown as cyan and purple
spheres, and water oxygens as red sphere.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS Lett
(2003,
544,
268-273)
copyright 2003.
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