This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1vyn

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

STRUCTURE AND NUCLEIC ACID BINDING OF THE DROSOPHILA ARGONAUTE2 PAZ DOMAIN

Structural highlights

1vyn is a 1 chain structure with sequence from Drosophila melanogaster. This structure supersedes the now removed PDB entry 1upo. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGO2_DROME Essential for RNA interference (RNAi); double-stranded RNA induces potent and specific gene silencing. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys or silences messenger RNAs homologous to the silencing trigger.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain.,Lingel A, Simon B, Izaurralde E, Sattler M Nature. 2003 Nov 27;426(6965):465-9. Epub 2003 Nov 16. PMID:14615801^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science. 2001 Aug 10;293(5532):1146-50. PMID:11498593 doi:http://dx.doi.org/10.1126/science.1064023
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vyn"

@@ Line 1: / Line 1: @@
 ==STRUCTURE AND NUCLEIC ACID BINDING OF THE DROSOPHILA ARGONAUTE2 PAZ DOMAIN==
-<StructureSection load='1vyn' size='340' side='right'caption='[[1vyn]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='1vyn' size='340' side='right'caption='[[1vyn]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vyn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1upo 1upo]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VYN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VYN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1vyn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1upo 1upo]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VYN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VYN FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1r6z|1r6z]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vyn OCA], [https://pdbe.org/1vyn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vyn RCSB], [https://www.ebi.ac.uk/pdbsum/1vyn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vyn ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AGO2_DROME AGO2_DROME] Essential for RNA interference (RNAi); double-stranded RNA induces potent and specific gene silencing. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multicomponent nuclease that destroys or silences messenger RNAs homologous to the silencing trigger.<ref>PMID:11498593</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Drome]]
+[[Category: Drosophila melanogaster]]
 [[Category: Large Structures]]
-[[Category: Izaurralde, E]]
+[[Category: Izaurralde E]]
-[[Category: Lingel, A]]
+[[Category: Lingel A]]
-[[Category: Sattler, M]]
+[[Category: Sattler M]]
-[[Category: Simon, B]]
+[[Category: Simon B]]
-[[Category: Nucleic acid binding]]
-[[Category: Rna interference]]

1vyn

From Proteopedia

Current revision

STRUCTURE AND NUCLEIC ACID BINDING OF THE DROSOPHILA ARGONAUTE2 PAZ DOMAIN

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox