1YTU: Structural Basis for 5'-end-specific Recognition of the Guide RNA Strand by the A. Fulgidus Piwi Protein

Citation:
Abstract
RNA interference (RNAi) is a conserved sequence-specific gene regulatory mechanism mediated by the RNA-induced silencing complex (RISC), which is composed of a single-stranded guide RNA and an Argonaute protein. The PIWI domain, a highly conserved motif within Argonaute, has been shown to adopt an RNase H fold critical for the endonuclease cleavage activity of RISC. Here we report the crystal structure of Archaeoglobus fulgidus Piwi protein bound to double-stranded RNA, thereby identifying the binding pocket for guide-strand 5'-end recognition and providing insight into guide-strand-mediated messenger RNA target recognition. The phosphorylated 5' end of the guide RNA is anchored within a highly conserved basic pocket, supplemented by the carboxy-terminal carboxylate and a bound divalent cation. The first nucleotide from the 5' end of the guide RNA is unpaired and stacks over a conserved tyrosine residue, whereas successive nucleotides form a four-base-pair RNA duplex. Mutation of the corresponding amino acids that contact the 5' phosphate in human Ago2 resulted in attenuated mRNA cleavage activity. Our structure of the Piwi-RNA complex, and that determined elsewhere, provide direct support for the 5' region of the guide RNA serving as a nucleation site for pairing with target mRNA and for a fixed distance separating the RISC-mediated mRNA cleavage site from the anchored 5' end of the guide RNA.
PDB ID: 1YTUDownload
MMDB ID: 107033
PDB Deposition Date: 2005/2/11
Updated in MMDB: 2013/02
Experimental Method:
x-ray diffraction
Resolution: 2.5  Å
Source Organism:
Archaeoglobus fulgidus DSM 4304
Similar Structures:
Biological Unit for 1YTU: trimeric; determined by author
Molecular Components in 1YTU
Label Count Molecule
Protein (1 molecule)
1
Hypothetical Protein Af1318(Gene symbol: AF_RS06655)
Molecule annotation
Nucleotides(2 molecules)
1
5'-r(p*ap*gp*ap*cp*ap*g)-3'
Molecule annotation
1
5'-r(p*up*gp*up*c)-3'
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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