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PDBsum entry 3luj
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RNA binding protein
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PDB id
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3luj
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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 for 5'-Nucleotide base-Specific recognition of guide RNA by human ago2.
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Authors
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F.Frank,
N.Sonenberg,
B.Nagar.
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Ref.
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Nature, 2010,
465,
818-822.
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PubMed id
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Abstract
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MicroRNAs (miRNAs) mediate post-transcriptional gene regulation through
association with Argonaute proteins (AGOs). Crystal structures of archaeal and
bacterial homologues of AGOs have shown that the MID (middle) domain mediates
the interaction with the phosphorylated 5' end of the miRNA guide strand and
this interaction is thought to be independent of the identity of the 5'
nucleotide in these systems. However, analysis of the known sequences of
eukaryotic miRNAs and co-immunoprecipitation experiments indicate that there is
a clear bias for U or A at the 5' position. Here we report the crystal structure
of a MID domain from a eukaryotic AGO protein, human AGO2. The structure, in
complex with nucleoside monophosphates (AMP, CMP, GMP, and UMP) mimicking the 5'
end of miRNAs, shows that there are specific contacts made between the base of
UMP or AMP and a rigid loop in the MID domain. Notably, the structure of the
loop discriminates against CMP and GMP and dissociation constants calculated
from NMR titration experiments confirm these results, showing that AMP (0.26 mM)
and UMP (0.12 mM) bind with up to 30-fold higher affinity than either CMP (3.6
mM) or GMP (3.3 mM). This study provides structural evidence for
nucleotide-specific interactions in the MID domain of eukaryotic AGO proteins
and explains the observed preference for U or A at the 5' end of miRNAs.
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