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PDBsum entry 1e2d
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Phosphotransferase
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PDB id
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1e2d
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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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Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate.
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Authors
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N.Ostermann,
I.Schlichting,
R.Brundiers,
M.Konrad,
J.Reinstein,
T.Veit,
R.S.Goody,
A.Lavie.
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Ref.
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Structure, 2000,
8,
629-642.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Thymidylate kinase (TMPK) is a nucleoside monophosphate kinase that
catalyzes the reversible phosphoryltransfer between ATP and TMP to yield ADP and
TDP. In addition to its vital role in supplying precursors for DNA synthesis,
human TMPK has an important medical role participating in the activation of a
number of anti-HIV prodrugs. RESULTS: Crystal structures of human TMPK in
complex with TMP and ADP, TMP and the ATP analog AppNHp, TMP with ADP and the
phosphoryl analog AlF(3), TDP and ADP, and the bisubstrate analog TP(5)A were
determined. The conformations of the P-loop, the LID region, and the
adenine-binding loop vary according to the nature of the complex. Substitution
of ADP by AppNHp results in partial closure of the P-loop and the rotation of
the TMP phosphate group to a catalytically unfavorable position, which rotates
back in the AlF(3) complex to a position suitable for in-line attack. In the
fully closed state observed in the TP(5)A and the TDP-ADP complexes, Asp15
interacts strongly with the 3'-hydroxyl group of TMP. CONCLUSIONS: The observed
changes of nucleotide state and conformation and the corresponding protein
structural changes are correlated with intermediates occurring along the
reaction coordinate and show the sequence of events occurring during phosphate
transfer. The low catalytic activity of human TMPK appears to be determined by
structural changes required to achieve catalytic competence and it is suggested
that a mechanism might exist to accelerate the activity.
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Figure 4.
Figure 4. Conformational changes of Arg97 and the
phosphoryl groups of TDP to the stable product conformation in
the TDP-ADP bound complex. Overlay of the TMP/TDP-binding site
of the structures of TMPK in complex with TMP, ADP and AlF[3]
(red) and TDP and ADP (yellow). In the complex with bound TDP
and ADP the sidechain of Arg97 rotates (90°) around the bond
between the atoms CG and CD such that it cannot act as a clamp
to bring both nucleotides together for the backward reaction.
The figures were generated using the programs Molscript [28] and
Raster 3D [29].
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2000,
8,
629-642)
copyright 2000.
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