8squ: Difference between revisions
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Monomeric MapSPARTA bound with guide RNA and target DNA hybrid== | |||
<StructureSection load='8squ' size='340' side='right'caption='[[8squ]], [[Resolution|resolution]] 3.28Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8squ]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Maribacter_polysiphoniae Maribacter polysiphoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SQU FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.28Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=8squ FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8squ OCA], [https://pdbe.org/8squ PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8squ RCSB], [https://www.ebi.ac.uk/pdbsum/8squ PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8squ ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A316E683_9FLAO A0A316E683_9FLAO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
While eukaryotic Argonautes and long prokaryotic Argonautes (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyze NAD(P)(+) to induce bacterial cell death(1). We present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Ago protein and an associated protein TIR-APAZ(2). SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA/DNA-bound state, two dimeric RNA/DNA-bound states, and a tetrameric RNA/DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. Apo SPARTA is inactive, its RNA/DNA-binding channel occupied an auto-inhibitory motif in TIR-APAZ. Upon RNA/DNA binding, SPARTA transitions from a monomer to a symmetric and then an asymmetric dimer, in which two TIR domains interact via charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolyzing NAD(P)(+). Additionally, we observed unique features of SPARTA-RNA/DNA interactions, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings contribute a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily. | |||
Oligomerization-mediated activation of a short prokaryotic Argonaute.,Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM Nature. 2023 Jul 26. doi: 10.1038/s41586-023-06456-z. PMID:37494956<ref>PMID:37494956</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8squ" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Maribacter polysiphoniae]] | |||
[[Category: Fu TM]] | |||
[[Category: Shen ZF]] | |||
[[Category: Yang XY]] | |||
Latest revision as of 08:56, 23 August 2023
Monomeric MapSPARTA bound with guide RNA and target DNA hybridMonomeric MapSPARTA bound with guide RNA and target DNA hybrid
Structural highlights
FunctionPublication Abstract from PubMedWhile eukaryotic Argonautes and long prokaryotic Argonautes (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyze NAD(P)(+) to induce bacterial cell death(1). We present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Ago protein and an associated protein TIR-APAZ(2). SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA/DNA-bound state, two dimeric RNA/DNA-bound states, and a tetrameric RNA/DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. Apo SPARTA is inactive, its RNA/DNA-binding channel occupied an auto-inhibitory motif in TIR-APAZ. Upon RNA/DNA binding, SPARTA transitions from a monomer to a symmetric and then an asymmetric dimer, in which two TIR domains interact via charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolyzing NAD(P)(+). Additionally, we observed unique features of SPARTA-RNA/DNA interactions, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings contribute a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily. Oligomerization-mediated activation of a short prokaryotic Argonaute.,Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM Nature. 2023 Jul 26. doi: 10.1038/s41586-023-06456-z. PMID:37494956[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||