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PDBsum entry 2ja9
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RNA binding protein
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PDB id
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2ja9
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References listed in PDB file
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Key reference
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Title
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Structural and biochemical characterization of the yeast exosome component rrp40.
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Authors
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A.Oddone,
E.Lorentzen,
J.Basquin,
A.Gasch,
V.Rybin,
E.Conti,
M.Sattler.
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Ref.
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EMBO Rep, 2007,
8,
63-69.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
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Abstract
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The exosome is a protein complex that is important in both degradation and
3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40
exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The
structure comprises an S1 domain and an unusual KH (K homology) domain. Close
packing of the S1 and KH domains is stabilized by a GxNG sequence, which is
uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal
the presence of a manganese-binding site at the interface of the two domains.
Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have
very low intrinsic affinity for RNA. The affinity of an archaeal core exosome
for RNA is significantly increased in the presence of the S1-KH subunit Rrp4,
indicating that multiple subunits might contribute to cooperative binding of RNA
substrates by the exosome.
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Figure 2.
Figure 2 Structure of Saccharomyces cerevisiae Rrp40  N.
(A) Crystal structure of S. cerevisiae Rrp40 N
(comprising residues 63–236). The S1 domain, the KH domain and
the conserved GxNG motif are indicated. (B) Superposition of the
structures of Rrp40 N
(magenta) and of AfRrp4 (orange; Büttner et al, 2005). The
two different GxxG sequence motifs present in AfRrp4 are
indicated. (C) Detailed view of the GxNG loop connecting  7
and 8
in the ScRrp40 KH domain. Hydrogen bonds formed by Asn 191
with residues of the S1 domain are indicated by dotted lines.
(D) View of the S1–KH domain interface. Conserved hydrophobic
side chains, which stabilize the domain interface, are shown in
black. Af, Archaeoglobus fulgidus.
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Figure 3.
Figure 3 Charge, conservation and interaction surfaces of Rrp40
N.
Molecular surface representations of Rrp40: left, the same view
as that depicted in Fig 2; right, rotated by 180° along a
vertical axis. (A) Molecular surfaces are coloured blue and red
according to positive and negative electrostatic potential,
respectively. (B) The degree of sequence conservation among
Rrp40 orthologues is mapped on the surface representation. Dark
or light green indicates residues that are fully or partially
conserved in Rrp40 orthologues, respectively (compare with Fig
1). (C) The conserved residues of the 3–
4
loop and the residues affected on addition of Mn^2+ are shown in
magenta and cyan, respectively. (D) Model of Rrp40 N
in the context of the exosome, obtained by replacing one of the
Rrp4 subunits in the structure of the Archaeoglobus fulgidus
(Af) exosome by Rrp40 N.
The conserved residues in the 3–
4
loop of the S1 domain and those affected by the addition
of Mn^2+ are shown in magenta and cyan, respectively. The
AfRrp41 and AfRrp42 subunits are shown in blue and green,
respectively, and the two AfRrp4 subunits are shown in orange.
Ribbon and surface representations were generated with PyMOL
(http://pymol.sourceforge.net).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO Rep
(2007,
8,
63-69)
copyright 2007.
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