Argonaute
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The Argonaute protein is a component of the RISC complex, central to the RNA-induced silencing in eukaryotic organisms [1]. 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 [2]. The third and final subclass, Wago, are worm specific. For more details see RNA Interference.
Structural OrganisationStructural 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 DomainPaz Domain
The is responsible for binding to the 3'-end overhangs of single-stranded RNAs and siRNA duplexes [3] and was shown to be essential for RISC activation [4]. 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 [5] ()
Piwi DomainPiwi 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 [6]. 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 [7]. Predictions point to for magnesium bivalent cations. However, in contrast to the findings in prokaryotic enzymes, eukaryotic structures were found lacking the metal [1].
RNA binding regionsRNA 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. with Y529 through base-stacking, along with hydrogen bonds to this same tyrosine residue, K533, N545 and K566. 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 [1].
3D Structures of argonaute3D Structures of argonaute
Updated on 10-February-2014
Argonaute 1Argonaute 1
1r4k – DmAGO1 PAZ domain – Drosophila melanogaster
1si2, 1si3 – hAGO1 PAZ domain + RNA - human
4kre, 4krf, 4kxt - hAGO1 + RNA
4g0p, 4g0x, 3vna – AtAGO1 MID domain – Arabidopsis thaliana
3vnb – AtAGO1 MID domain (mutant)
4g0q, 4g0y, 4g0z – AtAGO1 MID domain + nucleotide
Argonaute 2Argonaute 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
4ei1, 4ei3 – hAGO2 (mutant) + RNA
4f3t, 4ola, 4olb – hAGO2 + RNA
4g0m, 4g0o – AtAGO2 MID domain
ArgonauteArgonaute
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 – TtAGO + DNA – Thermus thermophilus
3hjf, 3hk2, 3ho1 – TtAGO (mutant) + DNA
External ResourcesExternal Resources
Animation showing the function of Argonaute during RNA interference
ReferencesReferences
- ↑ 1.0 1.1 1.2 Schirle NT, Macrae IJ. The Crystal Structure of Human Argonaute2. Science. 2012 Apr 26. PMID:22539551 doi:10.1126/science.1221551
- ↑ Hock J, Meister G. The Argonaute protein family. Genome Biol. 2008;9(2):210. Epub 2008 Feb 26. PMID:18304383 doi:10.1186/gb-2008-9-2-210
- ↑ Ma JB, Ye K, Patel DJ. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature. 2004 May 20;429(6989):318-22. PMID:15152257 doi:10.1038/nature02519
- ↑ Gu S, Jin L, Huang Y, Zhang F, Kay MA. Slicing-Independent RISC Activation Requires the Argonaute PAZ Domain. Curr Biol. 2012 Aug 21;22(16):1536-42. Epub 2012 Jul 12. PMID:22795694 doi:10.1016/j.cub.2012.06.040
- ↑ Lingel A, Simon B, Izaurralde E, Sattler M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature. 2003 Nov 27;426(6965):465-9. Epub 2003 Nov 16. PMID:14615801 doi:10.1038/nature02123
- ↑ Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ, Joshua-Tor L. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol. 2005 Apr;12(4):340-9. Epub 2005 Mar 30. PMID:15800637 doi:10.1038/nsmb918
- ↑ Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science. 2004 Sep 3;305(5689):1434-7. Epub 2004 Jul 29. PMID:15284453 doi:10.1126/science.1102514