PDBsum entry 3dlh

Nucleic acid binding protein/DNA

PDB id: 3dlh

Contents

Protein chains

673 a.a. *

DNA/RNA

Ligands

PGE

PO4 ×2

ACY ×2

Metals

_MG ×3

Waters ×75

* Residue conservation analysis

PDB id:

3dlh

Name:

Nucleic acid binding protein/DNA

Title:

Crystal structure of the guide-strand-containing argonaute protein silencing complex

Structure:

Argonaute. Chain: a, b. Engineered: yes. DNA (5'- d(dtp Dgp Dap Dgp Dgp Dtp Dap Dgp Dtp Dap Dgp Dgp Dtp Dtp Dgp Dtp Dap Dtp Dap Dgp Dt)-3'). Chain: x, y. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Gene: tt_p0026. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

3.00Å R-factor: 0.226 R-free: 0.284

Authors:

Y.Wang,G.Sheng,D.J.Patel

Key ref:

Y.Wang et al. (2008). Structure of the guide-strand-containing argonaute silencing complex. Nature, 456, 209-213. PubMed id: 18754009 DOI: 10.1038/nature07315

Date:

27-Jun-08 Release date: 02-Sep-08

Protein chains

Q746M7  (AGO_THET2) -  Protein argonaute from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)

Seq: 685 a.a.

Struc: 673 a.a.

DNA/RNA chains

T-G-A-G-G-T-A-G-T-A-G-G-A-T-A-G-T 17 bases

T-G-A-G-G-T-A-G-T-A-T-A-G-T 14 bases

Enzyme reactions

• Enzyme class: E.C.3.1.24.- - ?????

DOI no: 10.1038/nature07315

Nature 456:209-213 (2008)

PubMed id: 18754009

Structure of the guide-strand-containing argonaute silencing complex.

Y.Wang, G.Sheng, S.Juranek, T.Tuschl, D.J.Patel.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 456, 209-213) copyright 2008.

Figures were selected by an automated process.