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PDBsum entry 4acb
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References listed in PDB file
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Key reference
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Title
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Selenocysteine tRNA-Specific elongation factor selb is a structural chimaera of elongation and initiation factors.
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Authors
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M.Leibundgut,
C.Frick,
M.Thanbichler,
A.Böck,
N.Ban.
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Ref.
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EMBO J, 2005,
24,
11-22.
[DOI no: ]
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PubMed id
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Abstract
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In all three kingdoms of life, SelB is a specialized translation elongation
factor responsible for the cotranslational incorporation of selenocysteine into
proteins by recoding of a UGA stop codon in the presence of a downstream mRNA
hairpin loop. Here, we present the X-ray structures of SelB from the archaeon
Methanococcus maripaludis in the apo-, GDP- and GppNHp-bound form and use
mutational analysis to investigate the role of individual amino acids in its
aminoacyl-binding pocket. All three SelB structures reveal an EF-Tu:GTP-like
domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational
change of the Switch 2 region in the GTPase domain leads to the exposure of SelB
residues involved in clamping the 5' phosphate of the tRNA. A conserved extended
loop in domain III of SelB may be responsible for specific interactions with
tRNA(Sec) and act as a ruler for measuring the extra long acceptor arm. Domain
IV of SelB adopts a beta barrel fold and is flexibly tethered to domain III. The
overall domain arrangement of SelB resembles a 'chalice' observed so far only
for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome,
domain IV points towards the 3' mRNA entrance cleft ready to interact with the
downstream secondary structure element.
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Figure 1.
Figure 1 Overview of the SelB:GDP structure from M. maripaludis.
(A) Structure of SelB molecule C in the GDP conformation. The C
 trace
is rainbow coloured from the N- (blue) to the C-terminus
(orange). SelB consists of four individual domains, denoted I,
II, III and IV, which are arranged to form a 'molecular
chalice'. The first three domains form the cup and the fourth
the base of the chalice. The GDP nucleotide (red) is bound to
domain I (blue), which carries the GTPase activity. (B)
Flexibility of domain IV demonstrated by superposition of two
different SelB:GDP molecules (chains A and C) in the asymmetric
unit. The superposition of the first three domains shows that
domain IV is flexibly linked to domain III. Its orientation in
these two snapshots varies by an approximately 20° rotation.
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Figure 7.
Figure 7 Model of SelB bound to the GTPase activating centre of
the 70S ribosome prior to the release of the tRNA. (A)
Superposition of SelB domains I–III with the corresponding
domains from the EF-Tu:GDP:Phe-tRNA^Phe:kirromycin complex bound
to the 70S ribosome. After superposition of SelB (green) with
EF-Tu (red), SelB domain IV points towards the mRNA entrance
cleft of the small ribosomal subunit. The A/T state Phe-tRNA^Phe
from the EF-Tu complex is depicted in blue. CP: central
protuberance; L11: L11 region of the large subunit. (B) In the
schematic representation, the crown view of the 50S subunit is
shown (grey). Domain IV of SelB (green), which points towards
the mRNA entrance cleft formed by the 30S subunit (yellow
outline), would allow SelB to bind the SECIS element located in
the 3' UTR of the mRNA (red) either directly or via an adapter
protein. Sec-tRNA^Sec (blue) bound to SelB:GTP would recognize
the internal UGA stop codon located in the A site of the small
ribosomal subunit (shown as 'stop signal'). The usual UAA or UAG
stop codon of the gene is indicated with a red dot, and the
tRNAs located in the P and E sites are depicted in magenta and
brown, respectively. L1: large ribosomal protein L1; CP: central
protuberance; L11: L11 region of the large subunit.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2005,
24,
11-22)
copyright 2005.
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