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PDBsum entry 1it7
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of archaeosine tRNA-Guanine transglycosylase.
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Authors
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R.Ishitani,
O.Nureki,
S.Fukai,
T.Kijimoto,
N.Nameki,
M.Watanabe,
H.Kondo,
M.Sekine,
N.Okada,
S.Nishimura,
S.Yokoyama.
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Ref.
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J Mol Biol, 2002,
318,
665-677.
[DOI no: ]
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PubMed id
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Abstract
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Archaeosine tRNA-guanine transglycosylase (ArcTGT) catalyzes the exchange of
guanine at position 15 in the D-loop of archaeal tRNAs with a free
7-cyano-7-deazaguanine (preQ(0)) base, as the first step in the biosynthesis of
an archaea-specific modified base, archaeosine (7-formamidino-7-deazaguanosine).
We determined the crystal structures of ArcTGT from Pyrococcus horikoshii at 2.2
A resolution and its complexes with guanine and preQ(0), at 2.3 and 2.5 A
resolutions, respectively. The N-terminal catalytic domain folds into an
(alpha/beta)(8) barrel with a characteristic zinc-binding site, showing
structural similarity with that of the bacterial queuosine TGT (QueTGT), which
is involved in queuosine
(7-[[(4,5-cis-dihydroxy-2-cyclopenten-1-yl)-amino]methyl]-7-deazaguanosine)
biosynthesis and targets the tRNA anticodon. ArcTGT forms a dimer, involving the
zinc-binding site and the ArcTGT-specific C-terminal domain. The C-terminal
domains have novel folds, including an OB fold-like "PUA domain",
whose sequence is widely conserved in eukaryotic and archaeal RNA modification
enzymes. Therefore, the C-terminal domains may be involved in tRNA recognition.
In the free-form structure of ArcTGT, an alpha-helix located at the rim of the
(alpha/beta)(8) barrel structure is completely disordered, while it is ordered
in the guanine-bound and preQ(0)-bound forms. Structural comparison of the
ArcTGT.preQ(0), ArcTGT.guanine, and QueTGT.preQ(1) complexes provides novel
insights into the substrate recognition mechanisms of ArcTGT.
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Figure 3.
Figure 3. Domain architecture of the ArcTGT subunit. (a)
Ribbon diagram of the ArcTGT subunit. The catalytic domain,
domains C1, C2, and C3 are colored yellow, emerald green, sky
blue, and dark blue, respectively. Zinc and magnesium ions are
shown as metallic balls. (b) Topology diagram of the ArcTGT
structure. a-Helices are represented with circles or tubes, and
b-strands are shown with rectangles or arrows.
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Figure 7.
Figure 7. The catalytic domain of the preQ[0]-bound form of
(a) ArcTGT and (b) the base-free form of QueTGT. The viewpoints
of (a) and (b) are adjusted to that of Figure 6. The color of
helix a5 corresponds to the atomic B-factors, as indicated
below. The arrows indicate the major structural differences
between the ArcTGT and QueTGT, which are discussed in the text.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2002,
318,
665-677)
copyright 2002.
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