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2wac

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Extended Tudor domain of Drosophila Melanogaster Tudor-SN (p100)

Structural highlights

2wac is a 2 chain structure with sequence from Drosophila melanogaster. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SND1_DROME Endonuclease which shows activity towards both DNA and RNA substrates (PubMed:14508492, PubMed:26808625). Has a role in translation regulation throught its association with the with the RNA-induced silencing complex (RISC) (PubMed:14508492, PubMed:26808625). Plays a role in spermatogenesis probably by negatively regulating piwi expression in the germline (PubMed:26808625). Together with piwi, might be involved in transposon repression in the germline (PubMed:26808625).^[1] ^[2]

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

The Tudor-SN protein (p100, SND1) has been implicated in a variety of cellular processes, such as transcription, processing of edited double-stranded RNA, and splicing regulation. Molecular details of these functions are not yet understood. Tudor domains have previously been shown to bind methylated ligands, such as methylated lysines and arginines. It has been suggested that the role of Tudor-SN in splicing may involve binding to such methylated ligands or to the methylated 5' cap of spliceosomal snRNAs. Here, we report the crystal structure of the extended Tudor domain of Tudor-SN from Drosophila melanogaster to a resolution of 2.1 A. NMR secondary chemical shifts, relaxation data, and residual dipolar couplings indicate that the solution and crystal structures are similar. Binding of various ligands was investigated by NMR. Binding sites and affinities were characterized by chemical shift perturbations. We show that the aromatic cage of the Tudor domain specifically binds a peptide containing symmetrically dimethylated arginines (sDMA) with micromolar affinity, while the same peptide comprising nonmethylated arginines does not show significant chemical shift perturbations. Tudor-SN preferentially recognizes sDMA over asymmetrically dimethylated arginine (aDMA). In contrast, two 5' cap analogues with different methylation patterns, as well as mono-, di-, and trimethyllysines, show no binding. Our data demonstrate that the Tudor domain of Tudor-SN specifically recognizes sDMA-containing ligands. The aromatic cage of Tudor-SN is very similar to the one in the Tudor domain of the survival of motor neuron protein, which also recognizes sDMA peptides, indicating a conserved binding motif for this methylation mark. Recognition of sDMA in the C-terminal tails of spliceosomal Sm proteins suggests how Tudor-SN may interact with small nuclear ribonucleoprotein particles during the regulation of splicing.

Structure and ligand binding of the extended Tudor domain of D. melanogaster Tudor-SN.,Friberg A, Corsini L, Mourao A, Sattler M J Mol Biol. 2009 Apr 10;387(4):921-34. Epub 2009 Feb 14. PMID:19232356^[3]

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

References

↑ Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, Silva JM, Myers MM, Hannon GJ, Plasterk RH. A micrococcal nuclease homologue in RNAi effector complexes. Nature. 2003 Sep 25;425(6956):411-4. PMID:14508492 doi:10.1038/nature01956
↑ Ku HY, Gangaraju VK, Qi H, Liu N, Lin H. Tudor-SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila. PLoS Genet. 2016 Jan 25;12(1):e1005813. doi: 10.1371/journal.pgen.1005813., eCollection 2016 Jan. PMID:26808625 doi:http://dx.doi.org/10.1371/journal.pgen.1005813
↑ Friberg A, Corsini L, Mourao A, Sattler M. Structure and ligand binding of the extended Tudor domain of D. melanogaster Tudor-SN. J Mol Biol. 2009 Apr 10;387(4):921-34. Epub 2009 Feb 14. PMID:19232356 doi:10.1016/j.jmb.2009.02.018

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wac"

Categories: Drosophila melanogaster | Large Structures | Corsini L | Friberg A | Sattler M

@@ Line 1: / Line 1: @@
-==EXTENDED TUDOR DOMAIN OF DROSOPHILA MELANOGASTER TUDOR-SN (P100)==
-<StructureSection load='2wac' size='340' side='right' caption='[[2wac]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+==Extended Tudor domain of Drosophila Melanogaster Tudor-SN (p100)==
+<StructureSection load='2wac' size='340' side='right'caption='[[2wac]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WAC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wac]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WAC FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2wac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wac OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2wac RCSB], [http://www.ebi.ac.uk/pdbsum/2wac PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<table>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wac OCA], [https://pdbe.org/2wac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wac RCSB], [https://www.ebi.ac.uk/pdbsum/2wac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wac ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SND1_DROME SND1_DROME] Endonuclease which shows activity towards both DNA and RNA substrates (PubMed:14508492, PubMed:26808625). Has a role in translation regulation throught its association with the with the RNA-induced silencing complex (RISC) (PubMed:14508492, PubMed:26808625). Plays a role in spermatogenesis probably by negatively regulating piwi expression in the germline (PubMed:26808625). Together with piwi, might be involved in transposon repression in the germline (PubMed:26808625).<ref>PMID:14508492</ref> <ref>PMID:26808625</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wa/2wac_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wa/2wac_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2wac ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 23: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2wac" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 28: / Line 33: @@
 </StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Corsini, L.]]
+[[Category: Large Structures]]
-[[Category: Friberg, A.]]
+[[Category: Corsini L]]
-[[Category: Sattler, M.]]
+[[Category: Friberg A]]
-[[Category: Beta-barrel]]
+[[Category: Sattler M]]
-[[Category: Methylated arginine]]
-[[Category: Nuclease domain]]
-[[Category: P100]]
-[[Category: Sdma]]
-[[Category: Snd1]]
-[[Category: Splicing]]
-[[Category: Tudor]]
-[[Category: Tudor-sn]]
-[[Category: Unknown function]]

2wac

From Proteopedia

Current revision

Extended Tudor domain of Drosophila Melanogaster Tudor-SN (p100)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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