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PDBsum entry 1z3a
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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 kinetic characterization of escherichia coli tada, The wobble-Specific tRNA deaminase.
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Authors
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J.Kim,
V.Malashkevich,
S.Roday,
M.Lisbin,
V.L.Schramm,
S.C.Almo.
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Ref.
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Biochemistry, 2006,
45,
6407-6416.
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PubMed id
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Abstract
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The essential tRNA-specific adenosine deaminase catalyzes the deamination of
adenosine to inosine at the wobble position of tRNAs. This modification allows
for a single tRNA species to recognize multiple synonymous codons containing A,
C, or U in the last (3'-most) position and ensures that all sense codons are
appropriately decoded. We report the first combined structural and kinetic
characterization of a wobble-specific deaminase. The structure of the
Escherichia coli enzyme clearly defines the dimer interface and the coordination
of the catalytically essential zinc ion. The structure also identifies the
nucleophilic water and highlights residues near the catalytic zinc likely to be
involved in recognition and catalysis of polymeric RNA substrates. A minimal 19
nucleotide RNA stem substrate has permitted the first steady-state kinetic
characterization of this enzyme (k(cat) = 13 +/- 1 min(-)(1) and K(M) = 0.83 +/-
0.22 microM). A continuous coupled assay was developed to follow the reaction at
high concentrations of polynucleotide substrates (>10 microM). This work
begins to define the chemical and structural determinants responsible for
catalysis and substrate recognition and lays the foundation for detailed
mechanistic analysis of this essential enzyme.
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