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PDBsum entry 2qi2
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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 functional insights into dom34, A key component of no-Go mRNA decay.
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Authors
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H.H.Lee,
Y.S.Kim,
K.H.Kim,
I.Heo,
S.K.Kim,
O.Kim,
H.K.Kim,
J.Y.Yoon,
H.S.Kim,
D.O. .J.Kim,
S.J.Lee,
H.J.Yoon,
S.J.Kim,
B.G.Lee,
H.K.Song,
V.N.Kim,
C.M.Park,
S.W.Suh.
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Ref.
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Mol Cell, 2007,
27,
938-950.
[DOI no: ]
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PubMed id
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Abstract
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The yeast protein Dom34 is a key component of no-go decay, by which mRNAs with
translational stalls are endonucleolytically cleaved and subsequently degraded.
However, the identity of the endoribonuclease is unknown. Homologs of Dom34,
called Pelota, are broadly conserved in eukaryotes and archaea. To gain insights
into the structure and function of Dom34/Pelota, we have determined the
structure of Pelota from Thermoplasma acidophilum (Ta Pelota) and investigated
the ribonuclease activity of Dom34/Pelota. The structure of Ta Pelota is
tripartite, and its domain 1 has the RNA-binding Sm fold. We have discovered
that Ta Pelota has a ribonuclease activity and that its domain 1 is sufficient
for the catalytic activity. We also demonstrate that domain 1 of Dom34 has an
endoribonuclease activity against defined RNA substrates containing a stem loop,
which supports a direct catalytic role of yeast Dom34 in no-go mRNA decay.
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Figure 3.
Figure 3. Structural Comparison of Ta Pelota and the Sm
Protein from P. aerophilum
(A) Superposition of domain 1 of
Ta Pelota (magenta tube) and the P. aerophilum Sm protein
(orange tube) (PDB code 1I8F; Mura et al. [2001]). The conserved
Asn46 and Arg69 of the P. aerophilum Sm protein, termed
RNA-binding knuckles (Khusial et al., 2005), are shown.
(B)
Heptamer structure of the P. aerophilum Sm protein.
(C)
Schematic diagram comparing domain structures of Ta Pelota and
eRF1.
(D) Stereo 2F[o] − F[c] electron density map around
the Pro197-Gly198-Phe199 sequence of Ta Pelota.
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Figure 5.
Figure 5. Putative Active Site and Surface View of Ta Pelota
(A) Stereo ribbon diagram around the putative active site.
Three conserved acidic residues in motif I are shown.
(B)
Two different views of the electrostatic potential at the
molecular surface of Ta Pelota (blue, positive; red, negative).
They are roughly 90° apart. The location of conserved acidic
residues in motif I is indicated by the yellow dotted ellipse.
The green dotted ellipse on the right panel indicates the
positively charged surface patch next to sequence motif I.
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2007,
27,
938-950)
copyright 2007.
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