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PDBsum entry 3dlh
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Nucleic acid binding protein/DNA
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PDB id
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3dlh
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References listed in PDB file
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Key reference
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Title
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Structure of the guide-Strand-Containing argonaute silencing complex.
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Authors
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Y.Wang,
G.Sheng,
S.Juranek,
T.Tuschl,
D.J.Patel.
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Ref.
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Nature, 2008,
456,
209-213.
[DOI no: ]
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PubMed id
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Abstract
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The slicer activity of the RNA-induced silencing complex is associated with
argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated
sequence-specific cleavage of target messenger RNA. Here we report on the
crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated
21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel
positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like
conformational changes associated with complex formation. The bound guide strand
is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of
stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two
critically positioned arginines lock bases 10 and 11 at the cleavage site into
an unanticipated orthogonal alignment. Biochemical studies indicate that key
amino acid residues at the active site and those lining the 5'-phosphate-binding
pocket made up of the Mid domain are critical for cleavage activity, whereas
alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of
the PAZ domain show little effect.
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Figure 1.
Figure 1: Crystal structure of T. thermophilus argonaute bound
to a 5'-phosphorylated 21-base DNA guide strand. a, Stick
(DNA) and ribbon (Ago) view of the 3.0 Å structure of the
complex. Individual domains and linkers are colour-coded. The
bound 21-base DNA guide strand is coloured red (with phosphorus
atoms in yellow), and can be traced for nucleotides 1 to 11 and
18 to 21, together with phosphates at positions 16 and 17. b,
Corresponding stick (DNA) and electrostatically colour-coded
surface (Ago) view of the complex. c, An alternate stereo view
of the complex from that shown in a. For rotation of c, see
Supplementary Movie 2DLH.
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Figure 2.
Figure 2: Intermolecular hydrogen-bonding alignments in the T.
thermophilus Ago bound to a 21-base DNA guide strand. a,
Insertion of the 5'-phosphate of the DNA guide strand into the
binding pocket in the Mid domain. b, Positioning of stacked
3'-end residues 20 and 21 of the DNA guide strand into the
binding pocket in the PAZ domain. c, Positioning of stacked
residues 2 to 6 of the DNA guide strand, with emphasis on
intermolecular interactions. d, Positioning of stacked residues
6 to 10 and 11 of the DNA guide strand, with emphasis on
intermolecular interactions.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2008,
456,
209-213)
copyright 2008.
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