3s6w

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Tudor domain of human TDRD3

Structural highlights

3s6w is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.78Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TDRD3_HUMAN Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.^[1] ^[2] ^[3]

Publication Abstract from PubMed

SMN (Survival motor neuron protein) was characterized as a dimethyl-arginine binding protein over ten years ago. TDRD3 (Tudor domain-containing protein 3) and SPF30 (Splicing factor 30 kDa) were found to bind to various methyl-arginine proteins including Sm proteins as well later on. Recently, TDRD3 was shown to be a transcriptional coactivator, and its transcriptional activity is dependent on its ability to bind arginine-methylated histone marks. In this study, we systematically characterized the binding specificity and affinity of the Tudor domains of these three proteins quantitatively. Our results show that TDRD3 preferentially recognizes asymmetrical dimethylated arginine mark, and SMN is a very promiscuous effector molecule, which recognizes different arginine containing sequence motifs and preferentially binds symmetrical dimethylated arginine. SPF30 is the weakest methyl-arginine binder, which only binds the GAR motif sequences in our library. In addition, we also reported high-resolution crystal structures of the Tudor domain of TDRD3 in complex with two small molecules, which occupy the aromatic cage of TDRD3.

Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30.,Liu K, Guo Y, Liu H, Bian C, Lam R, Liu Y, Mackenzie F, Rojas LA, Reinberg D, Bedford MT, Xu RM, Min J PLoS One. 2012;7(2):e30375. Epub 2012 Feb 17. PMID:22363433^[4]

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

References

↑ Goulet I, Boisvenue S, Mokas S, Mazroui R, Cote J. TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. Hum Mol Genet. 2008 Oct 1;17(19):3055-74. doi: 10.1093/hmg/ddn203. Epub 2008 Jul , 15. PMID:18632687 doi:10.1093/hmg/ddn203
↑ Cote J, Richard S. Tudor domains bind symmetrical dimethylated arginines. J Biol Chem. 2005 Aug 5;280(31):28476-83. Epub 2005 Jun 6. PMID:15955813 doi:M414328200
↑ Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S, Bedford MT. TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell. 2010 Dec 22;40(6):1016-23. doi: 10.1016/j.molcel.2010.11.024. PMID:21172665 doi:10.1016/j.molcel.2010.11.024
↑ Liu K, Guo Y, Liu H, Bian C, Lam R, Liu Y, Mackenzie F, Rojas LA, Reinberg D, Bedford MT, Xu RM, Min J. Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30. PLoS One. 2012;7(2):e30375. Epub 2012 Feb 17. PMID:22363433 doi:10.1371/journal.pone.0030375

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3s6w"

Categories: Homo sapiens | Large Structures | Liu HP | Xu RM

@@ Line 1: / Line 1: @@
 ==Crystal structure of Tudor domain of human TDRD3==
-<StructureSection load='3s6w' size='340' side='right' caption='[[3s6w]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
+<StructureSection load='3s6w' size='340' side='right'caption='[[3s6w]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3s6w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S6W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3s6w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S6W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S6W FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TDRD3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></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=3s6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s6w RCSB], [http://www.ebi.ac.uk/pdbsum/3s6w PDBsum]</span></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=3s6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s6w OCA], [https://pdbe.org/3s6w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s6w RCSB], [https://www.ebi.ac.uk/pdbsum/3s6w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s6w ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TDRD3_HUMAN TDRD3_HUMAN] Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.<ref>PMID:18632687</ref> <ref>PMID:15955813</ref> <ref>PMID:21172665</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 13: / Line 16: @@
 Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30.,Liu K, Guo Y, Liu H, Bian C, Lam R, Liu Y, Mackenzie F, Rojas LA, Reinberg D, Bedford MT, Xu RM, Min J PLoS One. 2012;7(2):e30375. Epub 2012 Feb 17. PMID:22363433<ref>PMID:22363433</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3s6w" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 20: / Line 24: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Liu, H P.]]
+[[Category: Large Structures]]
-[[Category: Xu, R M.]]
+[[Category: Liu HP]]
-[[Category: Iso-propanol]]
+[[Category: Xu RM]]
-[[Category: Methylated arginine recognize]]
-[[Category: Transcription]]
-[[Category: Tudor]]

3s6w

From Proteopedia

Current revision

Crystal structure of Tudor domain of human TDRD3

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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