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PDBsum entry 2es6
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Gene regulation
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PDB id
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2es6
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References listed in PDB file
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Key reference
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Title
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Shape-Specific recognition in the structure of the vts1p sam domain with RNA.
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Authors
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F.C.Oberstrass,
A.Lee,
R.Stefl,
M.Janis,
G.Chanfreau,
F.H.Allain.
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Ref.
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Nat Struct Mol Biol, 2006,
13,
160-167.
[DOI no: ]
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PubMed id
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Abstract
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Although the abundant sterile alpha motif (SAM) domain was originally classified
as a protein-protein interaction domain, it has recently been shown that certain
SAM domains have the ability to bind RNA, defining a new type of
post-transcriptional gene regulator. To further understand the function of
SAM-RNA recognition, we determined the solution structures of the SAM domain of
the Saccharomyces cerevisiae Vts1p (Vts1p-SAM) and the Smaug response element
(SRE) stem-loop RNA as a complex and in isolation. The structures show that
Vts1p-SAM recognizes predominantly the shape of the SRE rather than its
sequence, with the exception of a G located at the tip of the pentaloop. Using
microarray gene profiling, we identified several genes in S. cerevisiae that
seem to be regulated by Vts1p and contain one or more copies of the SRE.
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Figure 3.
Figure 3. Solution structure of Vts1p-SAM domain bound to SRE
RNA and molecular basis of the recognition. (a)
Vts1p-SAM–SRE complex. Green, side chains important for
recognition; magenta dashed lines, possible hydrogen bonds. (b)
Stereo view of the most representative structure showing all the
interactions important for recognition, colored as in a. (c)
Schematic representation of the intermolecular interactions,
colored as in a. (d) Surface representation of the protein in
complex. Vts1p-SAM is colored by electrostatic potential (blue,
positive; red, negative) and the SRE RNA is shown in stick
representation.
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Figure 5.
Figure 5. Comparison of the Vts1p-SAM–SRE complex with the
structures of other SAM domain–containing proteins. (a)
Crystal structure of the RuvA SAM-like domain in complex DNA^45
(PDB entry 1C7Y); red and yellow helices correspond to those in
Vts1p-SAM shown in d. (b) Crystal structure of the heterodimer
formed by the Yan and Mae SAM domains^17 (1SV0), colored light
and dark gray, respectively. (c) Crystal structure of the
homodimer formed by the EphB2 SAM domain^18 (1B4F). (d) Overlay
of the Vts1p-SAM–SRE complex (blue, red and yellow) and the
crystal structure of Smaug (light green; 1OXJ) solved in its
free state^7.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2006,
13,
160-167)
copyright 2006.
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