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PDBsum entry 2osr
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RNA binding protein
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PDB id
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2osr
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References listed in PDB file
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Key reference
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Title
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Structure of the yeast sr protein npl3 and interaction with mRNA 3'-End processing signals.
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Authors
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P.Deka,
M.E.Bucheli,
C.Moore,
S.Buratowski,
G.Varani.
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Ref.
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J Mol Biol, 2008,
375,
136-150.
[DOI no: ]
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PubMed id
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Abstract
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Yeast Npl3 is homologous to SR proteins in higher eukaryotes, a family of
RNA-binding proteins that have multiple essential roles in RNA metabolism. This
protein competes with 3'-end processing factors for binding to the nascent RNA,
protecting the transcript from premature termination and coordinating
transcription termination and the packaging of the fully processed transcript
for export. The NMR structure of its RNA-binding domain shows two unusually
compact RNA recognition motifs (RRMs), and identifies the RNA recognition
surface in Npl3. Biochemical and NMR studies identify a class of G+U-rich RNA
sequences with high specificity for this protein. The protein binds to RNA and
forms a single globular structure, but the two RRMs of Npl3 are not equivalent,
with the second domain forming much stronger interactions with G+U-rich RNA
sequences that occur independently of the interaction of the first RRM. The
specific binding to G+U-rich RNAs observed for the two RRMs of Npl3 is masked in
the full-length protein by a much stronger but non-sequence-specific RNA-binding
activity residing outside of its RRMs. The preference of Npl3 for G+U-rich
sequences supports the model for its function in regulating recognition of
3'-end processing sites through competition with the Rna15 (yeast analog of
human CstF-64 protein) subunit of the processing complex.
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Figure 1.
Figure 1. Structure of Npl3. (a) Ribbon diagrams of the two
RRM domains of Npl3 as determined by NMR; the two domains are
structurally independent and connected by an eight residue
flexible linker. (b) and (c) Overlays of the 20 lowest energy
structures on the left, and ribbon representations of the lowest
energy structure on the right. Structures for RRM-1 and RRM-2
are shown in (b) and (c), respectively; the two domains are
shown separately here for clarity of presentation. (d) Amino
acid sequence for the full-length Npl3 protein. Residues
121–280 were the subject of NMR structure determination;
residues belonging to RRM-1 and RRM-2 are colored blue and pink,
respectively.
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Figure 2.
Figure 2. Structural comparison of the two RRM domains of
Npl3 to each other and to those of SxL protein (PDB 1B7F). (a)
Superposition of the structure of RRM-1 (gray) on RRM-2 (orange)
shows that the two domains are very similar, with an r.m.s.d.
between them of only 1.3 Å, despite the differences in the
loop between β2 and β3. (b) Superposition of the RRM-1 domain
of Npl3 (gray) with the RRM-1 domain of SxL (blue) gives an
r.m.s.d. of only 1.1 Å, while (c) superposition of the
RRM-2 domain of Npl3 (orange) with the RRM-2 domain of SxL
(green) gives an r.m.s.d. of 1.3 Å. The Figure was
generated using PyMOL [http://pymol.sourceforge.net/].
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The above figures are
reprinted
from an Open Access publication published by Elsevier:
J Mol Biol
(2008,
375,
136-150)
copyright 2008.
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