4qu4

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==Improved refinement of the Mtr4 apo crystal structure==
==Improved refinement of the Mtr4 apo crystal structure==
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<StructureSection load='4qu4' size='340' side='right' caption='[[4qu4]], [[Resolution|resolution]] 3.39&Aring;' scene=''>
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<StructureSection load='4qu4' size='340' side='right'caption='[[4qu4]], [[Resolution|resolution]] 3.39&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4qu4]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3l9o 3l9o]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QU4 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4qu4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3l9o 3l9o]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QU4 FirstGlance]. <br>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.392&#8491;</td></tr>
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<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>
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<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>
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<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=4qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qu4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qu4 RCSB], [http://www.ebi.ac.uk/pdbsum/4qu4 PDBsum]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4qu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qu4 OCA], [https://pdbe.org/4qu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qu4 RCSB], [https://www.ebi.ac.uk/pdbsum/4qu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qu4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/MTR4_YEAST MTR4_YEAST]] ATP-dependent RNA helicase required for the 3'-end formation of 5.8S RNA. Cofactor for the exosome complex that unwinds secondary structure in pre-rRNA. Required for nucleocytoplasmic transport of mRNA. May serve as a chaperone which translocates or normalizes the structure of mRNAs in preparation for export. Component of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates.<ref>PMID:15828860</ref>
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[https://www.uniprot.org/uniprot/MTR4_YEAST MTR4_YEAST] ATP-dependent RNA helicase required for the 3'-end formation of 5.8S RNA. Cofactor for the exosome complex that unwinds secondary structure in pre-rRNA. Required for nucleocytoplasmic transport of mRNA. May serve as a chaperone which translocates or normalizes the structure of mRNAs in preparation for export. Component of the TRAMP complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates.<ref>PMID:15828860</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3'-5' turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The 'ratchet helix' is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.
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The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding.,Taylor LL, Jackson RN, Rexhepaj M, King AK, Lott LK, van Hoof A, Johnson SJ Nucleic Acids Res. 2014 Nov 20. pii: gku1208. PMID:25414331<ref>PMID:25414331</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
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</div>
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*[[Helicase 3D structures|Helicase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: RNA helicase]]
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[[Category: Large Structures]]
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[[Category: Johnson, S J]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Taylor, L L]]
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[[Category: Johnson SJ]]
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[[Category: Antiparallel-coiled-coil]]
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[[Category: Taylor LL]]
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[[Category: Atp binding]]
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[[Category: Dshct domain]]
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[[Category: Helicase]]
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[[Category: Hydrolase]]
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[[Category: Nucleotide binding]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Rec-a fold]]
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[[Category: Rrna processing]]
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[[Category: Tramp]]
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[[Category: Winged-helix-turn-helix]]
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Current revision

Improved refinement of the Mtr4 apo crystal structure

PDB ID 4qu4

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