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5dnp

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Crystal structure of Mmi1 YTH domain

Structural highlights

5dnp is a 2 chain structure with sequence from Schizosaccharomyces pombe 972h-. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MMI1_SCHPO RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]^[1]

Publication Abstract from PubMed

The YTH domain-containing protein Mmi1, together with other factors, constitutes the machinery used to selectively remove meiosis-specific mRNA during the vegetative growth of fission yeast. Mmi1 directs meiotic mRNAs to the nuclear exosome for degradation by recognizing their DSR (determinant of selective removal) motif. Here, we present the crystal structure of the Mmi1 YTH domain in the apo state and in complex with a DSR motif, demonstrating that the Mmi1 YTH domain selectively recognizes the DSR motif. Intriguingly, Mmi1 also contains a potential m(6)A (N(6)-methyladenine)-binding pocket, but its binding of the DSR motif is dependent on a long groove opposite the m(6)A pocket. The DSR-binding mode is distinct from the m(6)A RNA-binding mode utilized by other YTH domains. Furthermore, the m(6)A pocket cannot bind m(6)A RNA. Our structural and biochemical experiments uncover the mechanism of the YTH domain in binding the DSR motif and help to elucidate the function of Mmi1.

A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1.,Wang C, Zhu Y, Bao H, Jiang Y, Xu C, Wu J, Shi Y Nucleic Acids Res. 2016 Jan 29;44(2):969-82. doi: 10.1093/nar/gkv1382. Epub 2015 , Dec 15. PMID:26673708^[2]

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

References

↑ Harigaya Y, Tanaka H, Yamanaka S, Tanaka K, Watanabe Y, Tsutsumi C, Chikashige Y, Hiraoka Y, Yamashita A, Yamamoto M. Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Nature. 2006 Jul 6;442(7098):45-50. PMID:16823445 doi:http://dx.doi.org/10.1038/nature04881
↑ Wang C, Zhu Y, Bao H, Jiang Y, Xu C, Wu J, Shi Y. A novel RNA-binding mode of the YTH domain reveals the mechanism for recognition of determinant of selective removal by Mmi1. Nucleic Acids Res. 2016 Jan 29;44(2):969-82. doi: 10.1093/nar/gkv1382. Epub 2015 , Dec 15. PMID:26673708 doi:http://dx.doi.org/10.1093/nar/gkv1382

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/5dnp"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Mmi1 YTH domain==
-<StructureSection load='5dnp' size='340' side='right' caption='[[5dnp]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5dnp' size='340' side='right'caption='[[5dnp]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5dnp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DNP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DNP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5dnp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DNP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5dno|5dno]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5dnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnp OCA], [http://pdbe.org/5dnp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dnp RCSB], [http://www.ebi.ac.uk/pdbsum/5dnp 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=5dnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dnp OCA], [https://pdbe.org/5dnp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dnp RCSB], [https://www.ebi.ac.uk/pdbsum/5dnp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dnp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO]] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>
+[https://www.uniprot.org/uniprot/MMI1_SCHPO MMI1_SCHPO] RNA-binding protein that recognizes and binds N6-methyladenosine (m6A)-containing RNAs, a modification present at internal sites of mRNAs and some non-coding RNAs (By similarity). Required for elemination of certain meiosis-specific mRNAs in an early event following transcription. May bind to the cis-acting region (DSR) of the mRNA, activating the nuclear exosome which may lead to the degradation of the transcript from the 3' region (PubMed:16823445).[UniProtKB:Q06390]<ref>PMID:16823445</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Shi, Y Y]]
+[[Category: Large Structures]]
-[[Category: Wang, C Y]]
+[[Category: Schizosaccharomyces pombe 972h-]]
-[[Category: Wu, J H]]
+[[Category: Shi YY]]
-[[Category: Zhu, Y W]]
+[[Category: Wang CY]]
-[[Category: Rna binding]]
+[[Category: Wu JH]]
-[[Category: Rna binding protein]]
+[[Category: Zhu YW]]

5dnp

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Current revision

Crystal structure of Mmi1 YTH domain

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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