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PDBsum entry 3e5c
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References listed in PDB file
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Key reference
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Title
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Crystal structures of the sam-Iii/s(mk) riboswitch reveal the sam-Dependent translation inhibition mechanism.
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Authors
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C.Lu,
A.M.Smith,
R.T.Fuchs,
F.Ding,
K.Rajashankar,
T.M.Henkin,
A.Ke.
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Ref.
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Nat Struct Biol, 2008,
15,
1076-1083.
[DOI no: ]
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PubMed id
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Abstract
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Three distinct classes of S-adenosyl-L-methionine (SAM)-responsive riboswitches
have been identified that regulate bacterial gene expression at the levels of
transcription attenuation or translation inhibition. The S(MK) box (SAM-III)
translational riboswitch has been identified in the SAM synthetase gene in
members of the Lactobacillales. Here we report the 2.2-A crystal structure of
the Enterococcus faecalis S(MK) box riboswitch. The Y-shaped riboswitch
organizes its conserved nucleotides around a three-way junction for SAM
recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing
with the anti-Shine-Dalgarno sequence in response to SAM binding, also directly
participates in SAM recognition. The riboswitch makes extensive interactions
with the adenosine and sulfonium moieties of SAM but does not appear to
recognize the tail of the methionine moiety. We captured a structural snapshot
of the S(MK) box riboswitch sampling the near-cognate ligand
S-adenosyl-L-homocysteine (SAH) in which SAH was found to adopt an alternative
conformation and fails to make several key interactions.
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Figure 3.
The labeling and base coloring scheme are consistent with
that in Figure 1. (a) Stereo view of the SAM binding site in the
S[MK] box riboswitch. The adenosine moiety of SAM is shown to
base-stack between U72 and G90. (b) The A73  circle
G90-C35 base triple paves the 'floor' of the SAM binding pocket.
The C-G base pair is co-planar, whereas A73 contacts from the
minor groove of G90 at a 45° tilted angle, which orients N6
of A73 for SAM recognition one base plane above.
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Figure 4.
(a) Stereo view of the binding pocket in the S[MK] box
riboswitch in complex with Se-SAM. The location of the selenium
atom is confirmed by the strong anomalous-difference density
shown in blue contoured at 8  .
The rest of the binding pocket in the Se-SAM–bound S[MK]
structure is almost identical to that in the SAM-bound
structure. Magenta mesh signifies the simulated composite omit
electron-density map of Se-SAM contoured at 1.5 .
(b) Stereo view of the SAH-bound S[MK] structure from a
direction similar to that shown in a. The simulated annealing
omit map contoured at 0.8 level
clearly shows that the ribose and sulfide moieties rotate
180° to exit the RNA from the linker helix side.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2008,
15,
1076-1083)
copyright 2008.
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Headers
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