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3fqd
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3fqd is ON HOLD Authors: Xiang, S., Cooper-Morgan, A., Jiao, X., Kiledjian, M., Manley, J., Tong, L. Description: Crystal Structure of the S. pombe...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal Structure of the S. pombe Rat1-Rai1 Complex== | |
| + | <StructureSection load='3fqd' size='340' side='right'caption='[[3fqd]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[3fqd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FQD FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
| + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fqg|3fqg]], [[3fqi|3fqi]], [[3fqj|3fqj]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dhp1, Rat1, SPAC26A3.12c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356]), din1, Rai1, SPAC19D5.06c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=3fqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqd OCA], [https://pdbe.org/3fqd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fqd RCSB], [https://www.ebi.ac.uk/pdbsum/3fqd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fqd ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [[https://www.uniprot.org/uniprot/XRN2_SCHPO XRN2_SCHPO]] Required for the processing of nuclear mRNA and rRNA precursors. May promote the termination of transcription by RNA polymerase II (By similarity). Essential for vegetative cell growth and chromosome segregation. Possesses 5'->3' exoribonuclease activity. [[https://www.uniprot.org/uniprot/DXO_SCHPO DXO_SCHPO]] 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 pyrophosphohydrolase 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 (By similarity). Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates. Stimulates exoribonuclease activity of rat1, allowing it to degrade RNAs with stable secondary structure more effectively.<ref>PMID:19194460</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/fq/3fqd_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/main_output.php?pdb_ID=3fqd ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The 5'-->3' exoribonucleases (XRNs) comprise a large family of conserved enzymes in eukaryotes with crucial functions in RNA metabolism and RNA interference. XRN2, or Rat1 in yeast, functions primarily in the nucleus and also has an important role in transcription termination by RNA polymerase II (refs 7-14). Rat1 exoribonuclease activity is stimulated by the protein Rai1 (refs 15, 16). Here we report the crystal structure at 2.2 A resolution of Schizosaccharomyces pombe Rat1 in complex with Rai1, as well as the structures of Rai1 and its murine homologue Dom3Z alone at 2.0 A resolution. The structures reveal the molecular mechanism for the activation of Rat1 by Rai1 and for the exclusive exoribonuclease activity of Rat1. Biochemical studies confirm these observations, and show that Rai1 allows Rat1 to degrade RNAs with stable secondary structure more effectively. There are large differences in the active site landscape of Rat1 compared to related and PIN (PilT N terminus) domain-containing nucleases. Unexpectedly, we identified a large pocket in Rai1 and Dom3Z that contains highly conserved residues, including three acidic side chains that coordinate a divalent cation. Mutagenesis and biochemical studies demonstrate that Rai1 possesses pyrophosphohydrolase activity towards 5' triphosphorylated RNA. Such an activity is important for messenger RNA degradation in bacteria, but this is, to our knowledge, the first demonstration of this activity in eukaryotes and suggests that Rai1/Dom3Z may have additional important functions in RNA metabolism. | ||
| - | + | Structure and function of the 5'-->3' exoribonuclease Rat1 and its activating partner Rai1.,Xiang S, Cooper-Morgan A, Jiao X, Kiledjian M, Manley JL, Tong L Nature. 2009 Apr 9;458(7239):784-8. Epub 2009 Feb 4. PMID:19194460<ref>PMID:19194460</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 3fqd" style="background-color:#fffaf0;"></div> | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Cbs 356]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Tong, L]] | ||
| + | [[Category: Xiang, S]] | ||
| + | [[Category: Exonuclease]] | ||
| + | [[Category: Hydrolase]] | ||
| + | [[Category: Hydrolase-protein binding complex]] | ||
| + | [[Category: Mrna processing]] | ||
| + | [[Category: Nuclease]] | ||
| + | [[Category: Nucleus]] | ||
| + | [[Category: Phosphoprotein]] | ||
| + | [[Category: Protein-protein complex]] | ||
| + | [[Category: Rrna processing]] | ||
| + | [[Category: Transcription]] | ||
| + | [[Category: Transcription regulation]] | ||
| + | [[Category: Transcription termination]] | ||
Current revision
Crystal Structure of the S. pombe Rat1-Rai1 Complex
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