Argonaute

spinqualitylabelsall models X-ray structure of the entire human Argonaute2 protein complex with RNA (red) (PDB 4ola) at 2.3Å resolution Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Function The Argonaute protein is a component of the RISC complex, central to the RNA-induced silencing in eukaryotic organisms . It is found in all higher eukaryotes and it plays an important role in a variety of processes as diverse as embryonic development, cell diferentiation and transposon silencing. These proteins are evolutionarily conserved and can be divided in three subfamilies: Ago, Piwi and Wago. The first are ubiquitously expressed and interact with siRNAs or miRNAs to participate in post-transcriptional gene silencing, both by destabilizing mRNA or by repressing the translation event. Piwi proteins are generally restricted to the germ line and associate piRNAs to mediate silencing of mobile genetic elements . The third and final subclass, Wago, are worm specific. For more details see RNA Interference. Structural Organisation There are two main structural features common to all Argonaute proteins: the Paz domain and the PIWI domain. Other structural features include the N domain and the Mid domain. Paz Domain The Paz Domain is responsible for binding to the 3'-end overhangs of single-stranded RNAs and siRNA duplexes and was shown to be essential for RISC activation . The domain is composed of two subdomains: the first is similar to the OB fold, a well known nucleic acid binding fold; the second subdomain is composed of a beta-hairpin followed by an alpha-helix. The cleft in between these two subdomains appears to interact with the 3' ends of ssRNA (See in structure) Piwi Domain The larger Piwi domain (~300 aminoacids) is found in a large number of related nucleic-acid binding proteins, in particular those involved in RNA binding and cleavage. In the Argonaute protein, its function is the dsRNA guided hydrolysis of ssRNA . PIWI is structurally an RNase H domain, and in Argonaute it servers as the 'Slicer', or the component responsible for cleaving the mRNA in the RISC complex . Predictions point to a putative binding site for magnesium bivalent cations. However, in contrast to the findings in prokaryotic enzymes, eukaryotic structures were found lacking the metal . RNA binding regions The majority of the RNA binding residues are located in the PIWI domain. The RNA molecule is bound in a conformation similar to DNA molecules in prokaryotic structures. The fact that the RNA bases 1 to 7 are well-defined in the electron density map hint at an uniform conformation of this region, perhaps forced by the protein. The 5' base of the RNA molecule interacts with Y529 through base-stacking, along with hydrogen bonds to this same tyrosine residue, K533, N545 and K566. Water mediates a couple of hydrogen bonds between the 5' phosphate and K570, R812 and the carboxyl group of A859. As such, the majority of the interactions between Argonaute and the RNA molecule are electrostatic in nature, arising from hydrogen bonding and salt bridges to the phosphate backbone. Van der Waals interactions between the ribose sugar ring and protein residues also contribute to the overall stabilization of the interaction. Residues S220, R357, R714 and R761 of the MID domain, together with a part of the PIWI domain bind the bases 7-9 .

3D Structures of argonaute

Updated on 15-March-2018

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• Argonaute 1
  • RNA-induced silencing – DmAGO1 PAZ domain – Drosophila melanogaster
    
  • RNA Interference, 1si3 – hAGO1 PAZ domain + RNA - human
    
  • 4kre, 4krf, 4kxt - hAGO1 + RNA
    
  • 5w6v - hAGO1 + RNA + protein GW1
    
  • 4g0p, 4g0x, 3vna – AtAGO1 MID domain – Arabidopsis thaliana
    
  • 3vnb – AtAGO1 MID domain (mutant)
    
  • 4g0q, 4g0y, 4g0z – AtAGO1 MID domain + nucleotide
    
• Argonaute 2
  • 1r6z – DmAGO2 PAZ domain/MBP
    
  • 1vyn – DmAGO2 PAZ domain - NMR
    
  • 1t2r, 1t2s – DmAGO2 PAZ domain + RNA - NMR
    
  • 3mj0 – DmAGO2 PAZ domain + RNA
    
  • 3luc, 3luk – hAGO2 MID domain
    
  • 3lud, 3lug, 3luh, 3luj, 3qx8, 3qx9 – hAGO2 MID domain + nucleotide
    
  • 4w5n, 4w5q, 4w5r, 4w5t, 5js1, 4z4i, 4z4h, 4z4g, 4z4f, 4z4e, 4z4d, 4z4c, 4ola, 5js2, 5wea – hAGO2 (mutant) + RNA
    
  • 4olb - hAGO2 (mutant) + RNA + tryptophan
    
  • 4f3t, 4w5o, 5t7b – hAGO2 + RNA
    
  • 5ki6 – hAGO2 + MIR-122
    
  • 4g0m, 4g0o – AtAGO2 MID domain
    
• Argonaute 3
  • 5vm9 – hAGO3 + RNA
    
• Argonaute
  • 1u04, 1z25, 1z26 – AGO (mutant) – Pyrococcus furiosus
    
  • 2f8s, 2f8t – AaAGO + RNA – Aquifex aeolicus
    
  • 2f8t, 2nub – AaAGO
    
  • 3da5 – AGO – Thermococcus thioreducens
    
  • 3dlb, 3dlh, 3f73, 3hm9, 3hvr, 3hxm, 4n41, 4n47, 4n76, 4nca, 4ncb, 5gq9 – TtAGO + DNA – Thermus thermophilus
    
  • 3hjf, 3hk2, 3ho1 – TtAGO (mutant) + DNA
    
  • 5i4a – MpAGO + RNA – Marinitoga piezophila
    
  • 5ux0 – MpAGO (mutant) + RNA + DNA
    
  • 5g5s – MjAGO – Methanocaldococcus jannaschii
    
  • 5g5t – MjAGO + DNA
    

External Resources

Uniprot: Q9UKV8

Wikipedia: Piwi Proteins

Wikipedia: Argonaute Proteins

Animation showing the function of Argonaute during RNA interference

Proteopedia Page Contributors and Editors (what is this?)

João Rodrigues, Michal Harel, Alexander Berchansky, Joel L. Sussman