PDBsum entry 1vyn

Nucleic acid binding

PDB id: 1vyn

Contents

Protein chain

117 a.a. *

* Residue conservation analysis

PDB id:

1vyn

Name:

Nucleic acid binding

Title:

Structure and nucleic acid binding of the drosophila argonaute2 paz domain

Structure:

Argonaute2. Chain: a. Fragment: paz domain, residues 605-743. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 469008.

NMR struc:

10 models

Authors:

A.Lingel,B.Simon,E.Izaurralde,M.Sattler

Key ref:

A.Lingel et al. (2003). Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature, 426, 465-469. PubMed id: 14615801 DOI: 10.1038/nature02123

Date:

03-May-04 Release date: 11-May-04

Supersedes:

1upo

Protein chain

Q9VUQ5  (AGO2_DROME) -  Protein argonaute-2 from Drosophila melanogaster

Seq: 1214 a.a.

Struc: 117 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/nature02123

Nature 426:465-469 (2003)

PubMed id: 14615801

Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain.

A.Lingel, B.Simon, E.Izaurralde, M.Sattler.

ABSTRACT

RNA interference is a conserved mechanism that regulates gene expression in response to the presence of double-stranded (ds)RNAs. The RNase III-like enzyme Dicer first cleaves dsRNA into 21-23-nucleotide small interfering RNAs (siRNAs). In the effector step, the multimeric RNA-induced silencing complex (RISC) identifies messenger RNAs homologous to the siRNAs and promotes their degradation. The Argonaute 2 protein (Ago2) is a critical component of RISC. Both Argonaute and Dicer family proteins contain a common PAZ domain whose function is unknown. Here we present the three-dimensional nuclear magnetic resonance structure of the Drosophila melanogaster Ago2 PAZ domain. This domain adopts a nucleic-acid-binding fold that is stabilized by conserved hydrophobic residues. The nucleic-acid-binding patch is located in a cleft between the surface of a central beta-barrel and a conserved module comprising strands beta3, beta4 and helix alpha3. Because critical structural residues and the binding surface are conserved, we suggest that PAZ domains in all members of the Argonaute and Dicer families adopt a similar fold with nucleic-acid binding function, and that this plays an important part in gene silencing.

Selected figure(s)

Figure 1.
Figure 1: Structure of the Ago2 PAZ domain from D. melanogaster. a, Stereoview of the ensemble of 15 lowest-energy NMR structures. Helices are shown in green, -strands in blue. Secondary structure elements are labelled by residue numbers (compare with Supplementary Fig. S1). b, Ribbon representation of the Ago2 PAZ domain. Secondary structure elements are labelled. The side chains of residues that were mutated are annotated and coloured in gold. c, Comparison of the central five-stranded -barrel of the PAZ domain to a canonical OB-fold in the E. coli Rho protein30. Related secondary structure elements are coloured in blue. The inserted 3, 4, 3 module of the PAZ domain is shown in orange. The respective topology of the two -barrels is indicated schematically at the bottom.

Figure 2.
Figure 2: Nucleic-acid-binding surface of the Ago2 PAZ domain. a, Surface representation of the PAZ domain coloured by sequence conservation (compare with Supplementary Fig. S1). High to low sequence conservation is coloured from magenta to white, respectively. b, Surface representation of the PAZ domain coloured by electrostatic charge. White, blue and red corresponds to neutral, positive and negative electrostatic potential, respectively. c, NMR titration of the PAZ domain with a single-stranded siRNA (siRNA-1as). The 1H-15N correlation spectrum of the free protein and at sixfold molar excess of siRNA is shown in blue and red, respectively. Green arrows indicate the direction of peak movements. The insert shows additional spectra at 0.5-, 1-, 1.5- and 3-fold molar excess of RNA. p.p.m., parts per million. d, RNA-binding site on the PAZ domain based on the NMR titration in c. Prolines or residues that could not be analysed owing to signal overlap are shown in yellow; residues where signals disappear at 1:0.5 molar protein:RNA ratio are coloured green. Other residues are coloured with a gradient from green to white according to the degree of chemical shift changes. In all panels the same orientation as in Fig. 1b is shown.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2003, 426, 465-469) copyright 2003.

Figures were selected by an automated process.