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PDBsum entry 2zxh
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Fad-binding protein
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PDB id
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2zxh
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References listed in PDB file
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Key reference
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Title
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Conserved cysteine residues of gida are essential for biogenesis of 5-Carboxymethylaminomethyluridine at tRNA anticodon.
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Authors
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T.Osawa,
K.Ito,
H.Inanaga,
O.Nureki,
K.Tomita,
T.Numata.
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Ref.
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Structure, 2009,
17,
713-724.
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PubMed id
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Abstract
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The 5-carboxymethylaminomethyl modification of uridine (cmnm(5)U) at the
anticodon first position occurs in tRNAs that read split codon boxes ending with
purine. This modification is crucial for correct translation, by restricting
codon-anticodon wobbling. Two conserved enzymes, GidA and MnmE, participate in
the cmnm(5)U modification process. Here we determined the crystal structure of
Aquifex aeolicus GidA at 2.3 A resolution. The structure revealed the tight
interaction of GidA with FAD. Structure-based mutation analyses allowed us to
identify two conserved Cys residues in the vicinity of the FAD-binding site that
are essential for the cmnm(5)U modification in vivo. Together with mutational
analysis of MnmE, we propose a mechanism for the cmnm(5)U modification process
where GidA, but not MnmE, attacks the C6 atom of uridine by a mechanism
analogous to that of thymidylate synthase. We also present a tRNA-docking model
that provides structural insights into the tRNA recognition mechanism for
efficient modification.
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