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PDBsum entry 2d6f
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Contents |
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424 a.a.
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485 a.a.
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522 a.a.
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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 basis of RNA-Dependent recruitment of glutamine to the genetic code.
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Authors
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H.Oshikane,
K.Sheppard,
S.Fukai,
Y.Nakamura,
R.Ishitani,
T.Numata,
R.L.Sherrer,
L.Feng,
E.Schmitt,
M.Panvert,
S.Blanquet,
Y.Mechulam,
D.Söll,
O.Nureki.
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Ref.
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Science, 2006,
312,
1950-1954.
[DOI no: ]
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PubMed id
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Abstract
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Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a
pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric
Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of
the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15
angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants
characterized the catalytic centers for the enzyme's three reactions
(glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel
for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln)
recognition by indirect readout based on shape complementarity of the D loop
suggests an early anticodon-independent RNA-based mechanism for adding glutamine
to the genetic code.
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Figure 1.
Fig. 1. Overall structure of the 1:1 complex of GatDE and
tRNA^Gln[1] (molecules B, D, and F). The protein domains are
colored differently; in GatD, the N-terminal domain, AnsA-like
domain 1, and AnsA-like domain 2 are shown in light green, blue,
and red, respectively; whereas in GatE, the AspRS-like insertion
domain, cradle domain, helical domain, and Yqey-like tail domain
are colored violet, cyan, orange, and pink, respectively. In the
present structure, the Yqey-like tail domain is shown as
translucent because its side chains are disordered, despite the
fact that the main chain was traced in the electron density map.
The bound tRNA molecules are yellow. In GatE, His15, Glu157, and
Glu184, which coordinate to an essential Mg2+ ion (red), are
shown to highlight the Glu-tRNA^Gln kinase and amidotransferase
sites. Gln240, which recognizes A73 (red), and Asp463, which
recognizes G52 (red), are indicated. All figures of the
molecular models were prepared with the program CueMol
(www.cuemol.org/).
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Figure 4.
Fig. 4. Ternary complex formation between GatE, GluRS, and
tRNA^Gln. Docking of T. thermophilus GluRS complexed with
tRNA^Glu (29) onto the present GatE·tRNA^Gln complex was
accomplished by superposing the complexed tRNA structures. In
GatDE, the AspRS-like insertion domain, cradle domain, helical
domain, and tail domain are colored violet, cyan, orange, and
pink, respectively. GluRS and tRNA are shown in gray and yellow,
respectively.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2006,
312,
1950-1954)
copyright 2006.
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