4gpu

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==Crystal structure of K. lactis Dxo1 (YDR370C) in complex with manganese==
==Crystal structure of K. lactis Dxo1 (YDR370C) in complex with manganese==
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<StructureSection load='4gpu' size='340' side='right' caption='[[4gpu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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<StructureSection load='4gpu' size='340' side='right'caption='[[4gpu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gpu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Kluyveromyces_lactis_nrrl_y-1140 Kluyveromyces lactis nrrl y-1140]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GPU FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gpu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GPU 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=MN:MANGANESE+(II)+ION'>MN</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]] 2.8&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gps|4gps]]</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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">KLLA0E02245g, KLLA0_E02245g ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284590 Kluyveromyces lactis NRRL Y-1140])</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=4gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gpu OCA], [https://pdbe.org/4gpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gpu RCSB], [https://www.ebi.ac.uk/pdbsum/4gpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gpu ProSAT]</span></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=4gpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gpu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gpu RCSB], [http://www.ebi.ac.uk/pdbsum/4gpu PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/DXO1_KLULA DXO1_KLULA] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs.<ref>PMID:22961381</ref>
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Recent studies showed that Rai1 is a crucial component of the mRNA 5'-end-capping quality-control mechanism in yeast. The yeast genome encodes a weak homolog of Rai1, Ydr370C, but little is known about this protein. Here we report the crystal structures of Ydr370C from Kluyveromyces lactis and the first biochemical and functional studies on this protein. The overall structure of Ydr370C is similar to Rai1. Ydr370C has robust decapping activity on RNAs with unmethylated caps, but it has no detectable pyrophosphohydrolase activity. Unexpectedly, Ydr370C also possesses distributive, 5'-3' exoRNase activity, and we propose the name Dxo1 for this new eukaryotic enzyme with both decapping and exonuclease activities. Studies of yeast in which both Dxo1 and Rai1 are disrupted reveal that mRNAs with incomplete caps are produced even under normal growth conditions, in sharp contrast to current understanding of the capping process.
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Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity.,Chang JH, Jiao X, Chiba K, Oh C, Martin CE, Kiledjian M, Tong L Nat Struct Mol Biol. 2012 Sep 9. doi: 10.1038/nsmb.2381. PMID:22961381<ref>PMID:22961381</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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</div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Kluyveromyces lactis nrrl y-1140]]
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[[Category: Kluyveromyces lactis NRRL Y-1140]]
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[[Category: Chang, J H]]
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[[Category: Large Structures]]
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[[Category: Chiba, K]]
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[[Category: Chang JH]]
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[[Category: Tong, L]]
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[[Category: Chiba K]]
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[[Category: 5'-3' exoribonuclease]]
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[[Category: Tong L]]
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[[Category: Decapping]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of K. lactis Dxo1 (YDR370C) in complex with manganese

PDB ID 4gpu

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