Argonaute: Difference between revisions
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The '''Argonaute''' protein is a component of the RISC complex, central to the [[RNA_Interference|RNA-induced silencing]] in eukaryotic organisms <ref name='ref1'>pmid 22539551</ref>. 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 <ref name='ref2'>pmid 18304383</ref>. The third and final subclass, Wago, are worm specific. | The '''Argonaute''' protein is a component of the RISC complex, central to the [[RNA_Interference|RNA-induced silencing]] in eukaryotic organisms <ref name='ref1'>pmid 22539551</ref>. 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 <ref name='ref2'>pmid 18304383</ref>. The third and final subclass, Wago, are worm specific. For more details see [[RNA Interference]]. | ||
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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. <scene name='Argonaute/Ago2-y529/5'>The 5' base of the RNA molecule interacts</scene> with Y529 through base-stacking, along with hydrogen bonds to this same tyrosine residue, K533, N545 and K566. <scene name='Argonaute/Ago2-water/4'>Water mediates a couple of hydrogen bonds</scene> 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 <ref name='ref1'/>. | 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. <scene name='Argonaute/Ago2-y529/5'>The 5' base of the RNA molecule interacts</scene> with Y529 through base-stacking, along with hydrogen bonds to this same tyrosine residue, K533, N545 and K566. <scene name='Argonaute/Ago2-water/4'>Water mediates a couple of hydrogen bonds</scene> 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 <ref name='ref1'/>. | ||
== 3D Structures of argonaute == | |||
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} | |||
===Argonaute 1=== | |||
[[1r4k]] – DmAGO1 PAZ domain – ''Drosophila melanogaster''<br /> | |||
[[1si2]], [[1si3]] – hAGO1 PAZ domain + RNA - human<br /> | |||
[[4g0p]], [[4g0x]], [[3vna]] – AtAGO1 MID domain – ''Arabidopsis thaliana''<br /> | |||
[[3vnb]] – AtAGO2 MID domain (mutant)<br /> | |||
[[4g0q]], [[4g0y]], [[4g0z]] – AtAGO2 MID domain + nucleotide<br /> | |||
===Argonaute 2=== | |||
[[1r6z]] – DmAGO2 PAZ domain/MBP <br /> | |||
[[1vyn]] – DmAGO2 PAZ domain - NMR <br /> | |||
[[1t2r]], [[1t2s]] – DmAGO2 PAZ domain + RNA - NMR<br /> | |||
[[3mj0]] – DmAGO2 PAZ domain + RNA <br /> | |||
[[3luc]], [[3luk]] – hAGO2 MID domain <br /> | |||
[[3lud]], [[3lug]], [[3luh]], [[3luj]], [[3qx8]], [[3qx9]] – hAGO2 MID domain + nucleotide<br /> | |||
[[4ei1]], [[4ei3]] – hAGO2 (mutant) + RNA <br /> | |||
[[4f3t]] – hAGO2 + RNA <br /> | |||
[[4g0m]], [[4g0o]] – AtAGO2 MID domain <br /> | |||
===Argonaute=== | |||
[[1u04]], [[1z25]], [[1z26]] – AGO (mutant) – ''Pyrococcus furiosus'' <br /> | |||
[[2f8s]], [[2f8t]] – AaAGO + RNA – ''Aquifex aeolicus''<br /> | |||
[[2f8t]] – AaAGO <br /> | |||
[[3da5]] – AGO – ''Thermococcus thioreducens''<br /> | |||
[[3dlb]], [[3dlh]], [[3f73]], [[3hm9]], [[3hvr]], [[3hxm]] – TtAGO + DNA – ''Thermus thermophilus''<br /> | |||
[[3hjf]], [[3hk2]], [[3ho1]] – TtAGO (mutant) + DNA <br /> | |||
==External Resources== | ==External Resources== | ||