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PDBsum entry 2jr4
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References listed in PDB file
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Key reference
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Title
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Anticodon domain modifications contribute order to tRNA for ribosome-Mediated codon binding.
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Authors
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F.A.Vendeix,
A.Dziergowska,
E.M.Gustilo,
W.D.Graham,
B.Sproat,
A.Malkiewicz,
P.F.Agris.
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Ref.
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Biochemistry, 2008,
47,
6117-6129.
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PubMed id
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Abstract
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The accuracy and efficiency with which tRNA decodes genomic information into
proteins require posttranscriptional modifications in or adjacent to the
anticodon. The modification uridine-5-oxyacetic acid (cmo (5)U 34) is found at
wobble position 34 in a single isoaccepting tRNA species for six amino acids,
alanine, leucine, proline, serine, threonine, and valine, each having 4-fold
degenerate codons. cmo (5)U 34 makes possible the decoding of 24 codons by just
six tRNAs. The contributions of this important modification to the structures
and codon binding affinities of the unmodified and fully modified anticodon stem
and loop domains of tRNA (Val3) UAC (ASL (Val3) UAC) were elucidated. The stems
of the unmodified ASL (Val3) UAC and that with cmo (5)U 34 and N
(6)-methyladenosine, m (6)A 37, adopted an A-form RNA conformation (rmsd
approximately 0.6 A) as determined with NMR spectroscopy and torsion-angle
molecular dynamics. However, the UV hyperchromicity, circular dichroism
ellipticity, and structural analyses indicated that the anticodon modifications
enhanced order in the loop. ASL (Val3) UAC-cmo (5)U 34;m (6)A 37 exhibited high
affinities for its cognate and wobble codons GUA and GUG, and for GUU in the
A-site of the programmed 30S ribosomal subunit, whereas the unmodified ASL
(Val3) UAC bound less strongly to GUA and not at all to GUG and GUU. Together
with recent crystal structures of ASL (Val3) UAC-cmo (5)U 34;m (6)A 37 bound to
all four of the valine codons in the A-site of the ribosome's 30S subunit, these
results clearly demonstrate that the xo (5)U 34-type modifications order the
anticodon loop prior to A-site codon binding for an expanded codon reading,
possibly reducing an entropic energy barrier to codon binding.
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Headers
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