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PDBsum entry 1pg0
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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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Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in escherichia coli methionyl-Trna synthetase.
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Authors
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T.Crepin,
E.Schmitt,
Y.Mechulam,
P.B.Sampson,
M.D.Vaughan,
J.F.Honek,
S.Blanquet.
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Ref.
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J Mol Biol, 2003,
332,
59-72.
[DOI no: ]
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PubMed id
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Abstract
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Binding of methionine to methionyl-tRNA synthetase (MetRS) is known to promote
conformational changes within the active site. However, the contribution of
these rearrangements to enzyme catalysis is not fully understood. In this study,
several methionine and methionyl adenylate analogues were diffused into crystals
of the monomeric form of Escherichia coli methionyl-tRNA synthetase. The
structures of the corresponding complexes were solved at resolutions below 1.9A
and compared to those of the enzyme free or complexed with methionine. Residues
Y15 and W253 play key roles in the strength of the binding of the amino acid and
of its analogues. Indeed, full motions of these residues are required to recover
the maximum in free energy of binding. Residue Y15 also controls the size of the
hydrophobic pocket where the amino acid side-chain interacts. H301 appears to
participate to the specific recognition of the sulphur atom of methionine.
Complexes with methionyl adenylate analogues illustrate the shielding by MetRS
of the region joining the methionine and adenosine moieties. Finally, the
structure of MetRS complexed to a methionine analogue mimicking the tetrahedral
carbon of the transition state in the aminoacylation reaction was solved. On the
basis of this model, we propose that, in response to the binding of the 3'-end
of tRNA, Y15 moves again in order to deshield the anhydride bond in the natural
adenylate.
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Figure 3.
Figure 3. Electronic densities associated with Y15 and
W253. A and B show the positions of W253 and Y15 in the free
enzyme[23.] (A) and in the MetRS:Met complex [16.] (B). C-F, The
final 2F[o] -F[c] electron density maps are represented. Each
map is contoured at 1s. C, MetRS:DFM complex; D, MetRS:TFM
complex; E, MetRS:MetI complex; F, MetRS:MetP complex. E, The
two alternative conformations of Y15 in the MetRS:MetI complex
are shown.
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Figure 4.
Figure 4. Binding of MetSA in the active site of MetRS. A,
Schematic representation of the main electrostatic interactions
between the enzyme and MetSA. Bottom: stereo views of active
site-bound MetSA (B), Metol-AMP (C) and methionine plus
adenosine (D). Only the enzyme residues relevant to the
discussion in the text are drawn.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
332,
59-72)
copyright 2003.
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