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PDBsum entry 2kbf
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References listed in PDB file
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Key reference
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Title
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Solution and crystal structures of mRNA exporter dbp5p and its interaction with nucleotides.
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Authors
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J.S.Fan,
Z.Cheng,
J.Zhang,
C.Noble,
Z.Zhou,
H.Song,
D.Yang.
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Ref.
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J Mol Biol, 2009,
388,
1.
[DOI no: ]
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PubMed id
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Abstract
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DEAD-box protein 5 (Dbp5p) plays very important roles in RNA metabolism from
transcription, to translation, to RNA decay. It is an RNA helicase and functions
as an essential RNA export factor from nucleus. Here, we report the solution NMR
structures of the N- and C-terminal domains (NTD and CTD, respectively) of Dbp5p
from Saccharomyces cerevisiae (ScDbp5p) and X-ray crystal structure of Dbp5p
from Schizosaccharomyces pombe (SpDbp5p) in the absence of nucleotides and RNA.
The crystal structure clearly shows that SpDbp5p comprises two RecA-like domains
that do not interact with each other. NMR results show that the N-terminal
flanking region of ScDpbp5 (M1-E70) is intrinsically unstructured and the region
Y71-R121 including the Q motif is highly dynamic on millisecond-microsecond
timescales in solution. The C-terminal flanking region of ScDbp5p forms a short
beta-strand and a long helix. This helix is unique for ScDbp5p and has not been
observed in other DEAD-box proteins. Compared with other DEAD-box proteins,
Dbp5p has an extra insert with six residues in the CTD. NMR structure reveals
that the insert is located in a solvent-exposed loop capable of interacting with
other proteins. ATP and ADP titration experiments show that both ADP and ATP
bind to the consensus binding site in the NTD of ScDbp5p but do not interact
with the CTD at all. Binding of ATP or ADP to NTD induces significant
conformational rearrangement too.
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Figure 1.
Fig. 1. Stereo views of 20 superimposed accepted structures
for NTD and CTD of ScDbp5p. The figure was generated using
MOLMOL.^40 Only backbone atoms (N, C^α, C′, and CO) were
chosen to superimpose the structures. (a) The region from Q81 to
T296 was drawn to represent the NTD structure. (b) The region
from T296 to D482 was drawn to represent the CTD structure.
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Figure 2.
Fig. 2. NMR and crystal structures of Dbp5p proteins. (a) NMR
structure of CTD of ScDbp5p. α-helices and β-strands are
colored cyan and magenta, respectively. The extreme C-terminal
helix in CTD is shown in red. The first residue number of CTD is
296. (b) NMR structure of NTD of ScDbp5p. The color coding is
the same as that in (a) with the exception that the N-terminal
extension region is shown in green. (c) Overall structure of
SpDbp5p solved by X-ray chromatography. The color coding is the
same as that in (a). (d) Stereo view of superposition of SpDbp5p
and HuDbp5p-ADP at the NTD. SpDbp5p is colored yellow and
HuDbp5p-ADP is in gray, with its N-terminal region in magenta
and the bound ADP in stick model. (e) Stereo view of
superposition of the NTD of ScDbp5p with that of HuDbp5p-ADP.
The N-terminal extension regions with residue numbers from 71 to
100 in ScDbp5p and from 53 to 100 in HuDbp5p are shown in green
and magenta, respectively. The positions of residues 71 and 90
are also labeled.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2009,
388,
1)
copyright 2009.
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