2vc8

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the LSm domain of human EDC3 (enhancer of decapping 3)

Structural highlights

2vc8 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 1.31Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

EDC3_HUMAN Binds single-stranded RNA. In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in spermiogenesis and oogenesis.^[1] ^[2] ^[3]

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

Members of the (L)Sm (Sm and Sm-like) protein family are found across all kingdoms of life and play crucial roles in RNA metabolism. The P-body component EDC3 (enhancer of decapping 3) is a divergent member of this family that functions in mRNA decapping. EDC3 is composed of a N-terminal LSm domain, a central FDF domain, and a C-terminal YjeF-N domain. We show that this modular architecture enables EDC3 to interact with multiple components of the decapping machinery, including DCP1, DCP2, and Me31B. The LSm domain mediates DCP1 binding and P-body localization. We determined the three-dimensional structures of the LSm domains of Drosophila melanogaster and human EDC3 and show that the domain adopts a divergent Sm fold that lacks the characteristic N-terminal alpha-helix and has a disrupted beta4-strand. This domain remains monomeric in solution and lacks several features that canonical (L)Sm domains require for binding RNA. The structures also revealed a conserved patch of surface residues that are required for the interaction with DCP1 but not for P-body localization. The conservation of surface and of critical structural residues indicates that LSm domains in EDC3 proteins adopt a similar fold that has separable novel functions that are absent in canonical (L)Sm proteins.

A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting.,Tritschler F, Eulalio A, Truffault V, Hartmann MD, Helms S, Schmidt S, Coles M, Izaurralde E, Weichenrieder O Mol Cell Biol. 2007 Dec;27(24):8600-11. Epub 2007 Oct 8. PMID:17923697^[4]

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

References

↑ Fenger-Gron M, Fillman C, Norrild B, Lykke-Andersen J. Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol Cell. 2005 Dec 22;20(6):905-15. PMID:16364915 doi:S1097-2765(05)01726-0
↑ Rudolph C, Sigruener A, Hartmann A, Orso E, Bals-Pratsch M, Gronwald W, Seifert B, Kalbitzer HR, Verdorfer I, Luetjens CM, Ortmann O, Bornstein SR, Schmitz G. ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis. Horm Metab Res. 2007 May;39(5):322-35. PMID:17533573 doi:10.1055/s-2007-977699
↑ Ling SH, Decker CJ, Walsh MA, She M, Parker R, Song H. Crystal structure of human Edc3 and its functional implications. Mol Cell Biol. 2008 Oct;28(19):5965-76. Epub 2008 Aug 4. PMID:18678652 doi:10.1128/MCB.00761-08
↑ Tritschler F, Eulalio A, Truffault V, Hartmann MD, Helms S, Schmidt S, Coles M, Izaurralde E, Weichenrieder O. A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting. Mol Cell Biol. 2007 Dec;27(24):8600-11. Epub 2007 Oct 8. PMID:17923697 doi:10.1128/MCB.01506-07

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/2vc8"

Categories: Homo sapiens | Large Structures | Hartmann MD | Tritschler F | Weichenrieder O

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF THE LSM DOMAIN OF HUMAN EDC3 (ENHANCER OF DECAPPING 3)==
-<StructureSection load='2vc8' size='340' side='right' caption='[[2vc8]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
+==Crystal structure of the LSm domain of human EDC3 (enhancer of decapping 3)==
+<StructureSection load='2vc8' size='340' side='right'caption='[[2vc8]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vc8]] 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=2VC8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VC8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vc8]] 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=2VC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VC8 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rm4|2rm4]]</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]] 1.31&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vc8 RCSB], [http://www.ebi.ac.uk/pdbsum/2vc8 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=2vc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vc8 OCA], [https://pdbe.org/2vc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vc8 RCSB], [https://www.ebi.ac.uk/pdbsum/2vc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vc8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/EDC3_HUMAN EDC3_HUMAN] Binds single-stranded RNA. In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in spermiogenesis and oogenesis.<ref>PMID:16364915</ref> <ref>PMID:17533573</ref> <ref>PMID:18678652</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/vc/2vc8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/2vc8_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=2vc8 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vc8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 29: / Line 33: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Hartmann, M D]]
+[[Category: Large Structures]]
-[[Category: Tritschler, F]]
+[[Category: Hartmann MD]]
-[[Category: Weichenrieder, O]]
+[[Category: Tritschler F]]
-[[Category: Enhancer of mrna decapping]]
+[[Category: Weichenrieder O]]
-[[Category: P-body component]]
-[[Category: Protein-binding]]
-[[Category: Rna]]
-[[Category: Sm-like protein]]

2vc8

From Proteopedia

Current revision

Crystal structure of the LSm domain of human EDC3 (enhancer of decapping 3)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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