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4db4

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Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex

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 ==Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex==
-<StructureSection load='4db4' size='340' side='right' caption='[[4db4]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
+<StructureSection load='4db4' size='340' side='right'caption='[[4db4]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4db4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DB4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4db4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DB4 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dax|4dax]], [[4daz|4daz]], [[4db2|4db2]]</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]] 3.599&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MSS116, YDR194C, YD9346.05C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=4db4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4db4 OCA], [https://pdbe.org/4db4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4db4 RCSB], [https://www.ebi.ac.uk/pdbsum/4db4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4db4 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></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=4db4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4db4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4db4 RCSB], [http://www.ebi.ac.uk/pdbsum/4db4 PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/MS116_YEAST MS116_YEAST] ATP-dependent RNA helicase required for mitochondrial splicing of group I and II introns. Specifically involved in the ATP-dependent splicing of the bl1 intron of COB. Also required for efficient mitochondrial translation.<ref>PMID:2535893</ref> <ref>PMID:7567443</ref> <ref>PMID:12402239</ref> <ref>PMID:15618406</ref>
-DEAD-box proteins are the largest family of nucleic acid helicases, and are crucial to RNA metabolism throughout all domains of life. They contain a conserved 'helicase core' of two RecA-like domains (domains (D)1 and D2), which uses ATP to catalyse the unwinding of short RNA duplexes by non-processive, local strand separation. This mode of action differs from that of translocating helicases and allows DEAD-box proteins to remodel large RNAs and RNA-protein complexes without globally disrupting RNA structure. However, the structural basis for this distinctive mode of RNA unwinding remains unclear. Here, structural, biochemical and genetic analyses of the yeast DEAD-box protein Mss116p indicate that the helicase core domains have modular functions that enable a novel mechanism for RNA-duplex recognition and unwinding. By investigating D1 and D2 individually and together, we find that D1 acts as an ATP-binding domain and D2 functions as an RNA-duplex recognition domain. D2 contains a nucleic-acid-binding pocket that is formed by conserved DEAD-box protein sequence motifs and accommodates A-form but not B-form duplexes, providing a basis for RNA substrate specificity. Upon a conformational change in which the two core domains join to form a 'closed state' with an ATPase active site, conserved motifs in D1 promote the unwinding of duplex substrates bound to D2 by excluding one RNA strand and bending the other. Our results provide a comprehensive structural model for how DEAD-box proteins recognize and unwind RNA duplexes. This model explains key features of DEAD-box protein function and affords a new perspective on how the evolutionarily related cores of other RNA and DNA helicases diverged to use different mechanisms.
-Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p.,Mallam AL, Del Campo M, Gilman B, Sidote DJ, Lambowitz AM Nature. 2012 Sep 2. doi: 10.1038/nature11402. PMID:22940866<ref>PMID:22940866</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: RNA helicase]]
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Campo, M Del]]
+[[Category: Del Campo M]]
-[[Category: Gilman, B D]]
+[[Category: Gilman BD]]
-[[Category: Lambowitz, A]]
+[[Category: Lambowitz A]]
-[[Category: Mallam, A L]]
+[[Category: Mallam AL]]
-[[Category: Sidote, D J]]
+[[Category: Sidote DJ]]
-[[Category: Dead-box]]
-[[Category: Hydrolase]]
-[[Category: Rna complex]]
-[[Category: Rna helicase]]
-[[Category: Rna-binding protein-dna]]

4db4

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Mss116p DEAD-box helicase domain 2 bound to a chimaeric RNA-DNA duplex

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