3fqd - Revision history

OCA at 08:07, 2 March 2022

2022-03-02T08:07:55Z

←Older revision		Revision as of 08:07, 2 March 2022
Line 1:		Line 1:

	==Crystal Structure of the S. pombe Rat1-Rai1 Complex==		==Crystal Structure of the S. pombe Rat1-Rai1 Complex==
-	<StructureSection load='3fqd' size='340' side='right' caption='[[3fqd]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='3fqd' size='340' side='right'caption='[[3fqd]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fqd]] is a 2 chain structure with sequence from [~~http~~://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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FQD FirstGlance]. <br>	+	<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"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</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='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">[[3fqg\|3fqg]], [[3fqi\|3fqi]], [[3fqj\|3fqj]]</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 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356]), din1, Rai1, SPAC19D5.06c ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3fqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqd OCA], [~~http~~://pdbe.org/3fqd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fqd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fqd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fqd ProSAT]</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=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>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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. [[~~http~~://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>	+	[[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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fq/3fqd_consurf.spt"</scriptWhenChecked>	+	<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>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Cbs 356]]		[[Category: Cbs 356]]
		+	[[Category: Large Structures]]
	[[Category: Tong, L]]		[[Category: Tong, L]]
	[[Category: Xiang, S]]		[[Category: Xiang, S]]

OCA at 18:08, 5 August 2016

2016-08-05T18:08:34Z

←Older revision		Revision as of 18:08, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the S. pombe Rat1-Rai1 Complex==		==Crystal Structure of the S. pombe Rat1-Rai1 Complex==
	<StructureSection load='3fqd' size='340' side='right' caption='[[3fqd]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3fqd' size='340' side='right' caption='[[3fqd]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3fqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Schizosaccharomyces_pombe Schizosaccharomyces pombe~~]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FQD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3fqd]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FQD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='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">[[3fqg\|3fqg]], [[3fqi\|3fqi]], [[3fqj\|3fqj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fqg\|3fqg]], [[3fqi\|3fqi]], [[3fqj\|3fqj]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhp1, Rat1, SPAC26A3.12c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 ~~Schizosaccharomyces pombe~~]), din1, Rai1, SPAC19D5.06c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 ~~Schizosaccharomyces pombe~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhp1, Rat1, SPAC26A3.12c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356]), din1, Rai1, SPAC19D5.06c ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3fqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fqd RCSB], [http://www.ebi.ac.uk/pdbsum/3fqd PDBsum]</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=3fqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqd OCA], [http://pdbe.org/3fqd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fqd RCSB], [http://www.ebi.ac.uk/pdbsum/3fqd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fqd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://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. [[http://www.uniprot.org/uniprot/~~DOM3Z_SCHPO DOM3Z_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>	+	[[http://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. [[http://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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3fqd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Schizosaccharomyces pombe~~]]	+	[[Category: Cbs 356]]
	[[Category: Tong, L]]		[[Category: Tong, L]]
	[[Category: Xiang, S]]		[[Category: Xiang, S]]

OCA at 20:51, 25 December 2014

2014-12-25T20:51:56Z

←Older revision		Revision as of 20:51, 25 December 2014
Line 9:		Line 9:
	<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=3fqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fqd RCSB], [http://www.ebi.ac.uk/pdbsum/3fqd PDBsum]</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=3fqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fqd RCSB], [http://www.ebi.ac.uk/pdbsum/3fqd PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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. [[http://www.uniprot.org/uniprot/DOM3Z_SCHPO DOM3Z_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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:28, 3 December 2014

2014-12-03T10:28:21Z

←Older revision		Revision as of 10:28, 3 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3fqd.~~png~~\|~~left~~\|200px]]	+	==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 [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FQD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[3fqg\|3fqg]], [[3fqi\|3fqi]], [[3fqj\|3fqj]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dhp1, Rat1, SPAC26A3.12c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe]), din1, Rai1, SPAC19D5.06c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 Schizosaccharomyces pombe])</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=3fqd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fqd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fqd RCSB], [http://www.ebi.ac.uk/pdbsum/3fqd PDBsum]</span></td></tr>
		+	</table>
		+	== 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/chain_selection.php?pdb_ID=2ata 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_3fqd\| PDB=3fqd \| SCENE= }}~~	+	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>

-	~~===Crystal Structure~~ of the S. ~~pombe Rat1-Rai1 Complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19194460}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3fqd]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019194460<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
-	[[Category: Tong, L.]]	+	[[Category: Tong, L]]
-	[[Category: Xiang, S.]]	+	[[Category: Xiang, S]]
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA: Protected "3fqd" [edit=sysop:move=sysop]

2013-02-20T14:49:37Z

Protected "3fqd" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:49, 20 February 2013

OCA at 14:49, 20 February 2013

2013-02-20T14:49:34Z

←Older revision		Revision as of 14:49, 20 February 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3fqd.png\|left\|200px]]		[[Image:3fqd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3fqd", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3fqd\| PDB=3fqd \| SCENE= }}		{{STRUCTURE_3fqd\| PDB=3fqd \| SCENE= }}

	===Crystal Structure of the S. pombe Rat1-Rai1 Complex===		===Crystal Structure of the S. pombe Rat1-Rai1 Complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19194460}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19194460 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19194460}}		{{ABSTRACT_PUBMED_19194460}}

	==About this Structure==		==About this Structure==
-	~~3FQD~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQD OCA].	+	[[3fqd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19194460~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019194460</ref><references group="xtra"/>
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
	[[Category: Tong, L.]]		[[Category: Tong, L.]]
Line 29:		Line 17:
	[[Category: Exonuclease]]		[[Category: Exonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
-	[[Category: Hydrolase/protein binding complex]]	+	[[Category: Hydrolase-protein binding complex]]
	[[Category: Mrna processing]]		[[Category: Mrna processing]]
	[[Category: Nuclease]]		[[Category: Nuclease]]
Line 39:		Line 27:
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Transcription termination]]		[[Category: Transcription termination]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 29 21:02:25 2009''

OCA at 18:02, 29 April 2009

2009-04-29T18:02:26Z

←Older revision		Revision as of 18:02, 29 April 2009
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3fqd.~~jpg~~\|left\|200px]]	+	[[Image:3fqd.png\|left\|200px]]

	<!--		<!--
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	===Crystal Structure of the S. pombe Rat1-Rai1 Complex===		===Crystal Structure of the S. pombe Rat1-Rai1 Complex===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19194460}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19194460 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19194460}}

	==About this Structure==		==About this Structure==
	3FQD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQD OCA].		3FQD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQD OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19194460</ref><references group="xtra"/>
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
	[[Category: Tong, L.]]		[[Category: Tong, L.]]
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	[[Category: Transcription termination]]		[[Category: Transcription termination]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 4 11~~:42:19 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 29 21:02:25 2009''

OCA at 09:42, 4 February 2009

2009-02-04T09:42:21Z

←Older revision		Revision as of 09:42, 4 February 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3fqd.jpg\|left\|200px]]

-	The ~~entry 3fqd~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3fqd", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3fqd\| PDB=3fqd \| SCENE= }}

-	~~Authors: Xiang,~~ S.~~, Cooper~~-~~Morgan, A., Jiao, X., Kiledjian, M., Manley, J., Tong, L.~~	+	===Crystal Structure of the S. pombe Rat1-Rai1 Complex===

-	Description: Crystal Structure of the S. pombe Rat1-Rai1 Complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jan 14 12~~:55:58 2009''	+	==About this Structure==
		+	3FQD is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FQD OCA].
		+	[[Category: Schizosaccharomyces pombe]]
		+	[[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]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 4 11:42:19 2009''

OCA: 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...

2009-01-14T10:55:58Z

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...

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 Rat1-Rai1 Complex

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 12:55:58 2009''