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PDBsum entry 2mst
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RNA binding protein
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PDB id
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2mst
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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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Structure, Backbone dynamics and interactions with RNA of the c-Terminal RNA-Binding domain of a mouse neural RNA-Binding protein, Musashi1.
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Authors
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T.Nagata,
R.Kanno,
Y.Kurihara,
S.Uesugi,
T.Imai,
S.Sakakibara,
H.Okano,
M.Katahira.
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Ref.
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J Mol Biol, 1999,
287,
315-330.
[DOI no: ]
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PubMed id
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Abstract
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Musashi1 is an RNA-binding protein abundantly expressed in the developing mouse
central nervous system. Its restricted expression in neural precursor cells
suggests that it is involved in the regulation of asymmetric cell division.
Musashi1 contains two ribonucleoprotein (RNP)-type RNA-binding domains (RBDs),
RBD1 and RBD2. Our previous studies showed that RBD1 alone binds to RNA, while
the binding of RBD2 is not detected under the same conditions. Joining of RBD2
to RBD1, however, increases the affinity to greater than that of RBD1 alone,
indicating that RBD2 contributes to RNA-binding. We have determined the
three-dimensional solution structure of the C-terminal RBD (RBD2) of Musashi1 by
NMR. It folds into a compact alpha beta structure comprising a four-stranded
antiparallel beta-sheet packed against two alpha-helices, which is
characteristic of RNP-type RBDs. Special structural features of RBD2 include a
beta-bulge in beta2 and a shallow twist of the beta-sheet. The smaller 1H-15N
nuclear Overhauser enhancement values for the residues of loop 3 between beta2
and beta3 suggest that this loop is flexible in the time-scale of nano- to
picosecond order. The smaller 15N T2 values for the residues around the border
between alpha2 and the following loop (loop 5) suggest this region undergoes
conformational exchange in the milli- to microsecond time-scale. Chemical shift
perturbation analysis indicated that RBD2 binds to an RNA oligomer obtained by
in vitro selection under the conditions for NMR measurements, and thus the
nature of the weak RNA-binding of RBD2 was successfully characterized by NMR,
which is otherwise difficult to assess. Mainly the residues of the surface
composed of the four-stranded beta-sheet, loops and C-terminal region are
involved in the interaction. The appearance of side-chain NH proton resonances
of arginine residues of loop 3 and imino proton resonances of RNA bases upon
complex formation suggests the formation of intermolecular hydrogen bonds. The
structural arrangement of the rings of the conserved aromatic residues of beta2
and beta3 is suitable for stacking interaction with RNA bases, known to be one
of the major protein-RNA interactions, but a survey of the perturbation data
suggested that the stacking interaction is not ideally achieved in the complex,
which may be related to the weaker RNA-binding of RBD2.
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Figure 3.
Figure 3. The four-stranded antiparallel β-sheet of RBD2.
Interstrand NOEs are indicated by double-headed continuous
arrows, the NOEs with ambiguity due to overlapping being
indicated by double-headed broken arrows. Slowly exchanging
amide protons are indicated by bold H. Hydrogen bonds consistent
with the NOEs and exchange data are indicated by broken lines.
Black boxes on C^α indicate that the side-chains of these
residues are presumed to point inside the protein.
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Figure 4.
Figure 4. The structure of RBD2. (a) Superposition of the
main-chains of 20 refined structures. N and C indicate K110 and
A184, respectively, and loop 3 is labeled. (b) Schematic drawing
of the restrained energy minimized mean structure derived from
the 20 refined structures, as viewed from the same direction as
that in (a). (c) Hydrophobic core. Overlaying of the 20
structures of the side-chains for residues involved in the
hydrophobic core is shown on the main-chain of the restrained
energy minimized mean structure. α-Helices and β-strands are
colored red and sky-blue, respectively. (d) Hydrophobic patch
exposed to the solvent. The same overlaying as that in (c) is
shown for F112, F152 and F154, being rotated by ca 90 ° from
that in (c).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1999,
287,
315-330)
copyright 1999.
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Secondary reference #1
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Title
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Structural properties and RNA-Binding activities of two RNA recognition motifs of a mouse neural RNA-Binding protein, Mouse-Musashi-1.
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Authors
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Y.Kurihara,
T.Nagata,
T.Imai,
A.Hiwatashi,
M.Horiuchi,
S.Sakakibara,
M.Katahira,
H.Okano,
S.Uesugi.
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Ref.
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Gene, 1997,
186,
21-27.
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PubMed id
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