2a8s - Revision history

OCA at 07:20, 23 August 2023

2023-08-23T07:20:52Z

←Older revision		Revision as of 07:20, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='2a8s' size='340' side='right'caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2a8s' size='340' side='right'caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~African_clawed_frog African clawed frog~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A8S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GTP:GUANOSINE~~-~~5-TRIPHOSPHATE'>GTP</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~</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]] 2.45Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~YCM~~:S-(2-~~AMINO-2-OXOETHYL)-L-CYSTEINE~~'>~~YCM~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</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;~~'>~~[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]~~</~~div~~></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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [https://pdbe.org/2a8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [https://www.ebi.ac.uk/pdbsum/2a8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a8s 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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [https://pdbe.org/2a8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [https://www.ebi.ac.uk/pdbsum/2a8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a8s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NUD16_XENLA NUD16_XENLA]] RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.<ref>PMID:15053875</ref> <ref>PMID:10585477</ref> <ref>PMID:17567574</ref> <ref>PMID:18820299</ref>	+	[https://www.uniprot.org/uniprot/NUD16_XENLA NUD16_XENLA] RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.<ref>PMID:15053875</ref> <ref>PMID:10585477</ref> <ref>PMID:17567574</ref> <ref>PMID:18820299</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: African clawed frog]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Peculis, B A~~]]	+	[[Category: Xenopus laevis]]
-	[[Category: ~~Scarsdale, J N~~]]	+	[[Category: Peculis BA]]
-	[[Category: ~~Wright, H T~~]]	+	[[Category: Scarsdale JN]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Wright HT]]
-	~~[[Category: Modified nudix hydrolase fold]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 09:38, 5 May 2021

2021-05-05T09:38:41Z

←Older revision		Revision as of 09:38, 5 May 2021
Line 3:		Line 3:
	<StructureSection load='2a8s' size='340' side='right'caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2a8s' size='340' side='right'caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2A8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A8S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</div></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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [~~http~~://pdbe.org/2a8s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2a8s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2a8s 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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [https://pdbe.org/2a8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [https://www.ebi.ac.uk/pdbsum/2a8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a8s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NUD16_XENLA NUD16_XENLA]] RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.<ref>PMID:15053875</ref> <ref>PMID:10585477</ref> <ref>PMID:17567574</ref> <ref>PMID:18820299</ref>	+	[[https://www.uniprot.org/uniprot/NUD16_XENLA NUD16_XENLA]] RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.<ref>PMID:15053875</ref> <ref>PMID:10585477</ref> <ref>PMID:17567574</ref> <ref>PMID:18820299</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:10, 24 July 2019

2019-07-24T07:10:00Z

←Older revision		Revision as of 07:10, 24 July 2019
Line 1:		Line 1:

	==2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP==		==2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP==
-	<StructureSection load='2a8s' size='340' side='right' caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='2a8s' size='340' side='right'caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8S FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8S FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: African clawed frog]]		[[Category: African clawed frog]]
		+	[[Category: Large Structures]]
	[[Category: Peculis, B A]]		[[Category: Peculis, B A]]
	[[Category: Scarsdale, J N]]		[[Category: Scarsdale, J N]]

OCA at 07:27, 9 May 2018

2018-05-09T07:27:41Z

←Older revision		Revision as of 07:27, 9 May 2018
Line 1:		Line 1:
		+
	==2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP==		==2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP==
	<StructureSection load='2a8s' size='340' side='right' caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2a8s' size='340' side='right' caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [http://pdbe.org/2a8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [http://www.ebi.ac.uk/pdbsum/2a8s 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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [http://pdbe.org/2a8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [http://www.ebi.ac.uk/pdbsum/2a8s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2a8s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a8/2a8s_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a8/2a8s_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>

OCA at 03:55, 10 February 2016

2016-02-10T03:55:25Z

←Older revision		Revision as of 03:55, 10 February 2016
Line 18:		Line 18:
	<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=2a8s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:08, 11 September 2015

2015-09-11T05:08:18Z

←Older revision		Revision as of 05:08, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2a8s' size='340' side='right' caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2a8s' size='340' side='right' caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Xenopus_laevis Xenopus laevis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [http://www.ebi.ac.uk/pdbsum/2a8s 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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [http://pdbe.org/2a8s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [http://www.ebi.ac.uk/pdbsum/2a8s PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2a8s" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Xenopus laevis~~]]	+	[[Category: African clawed frog]]
	[[Category: Peculis, B A]]		[[Category: Peculis, B A]]
	[[Category: Scarsdale, J N]]		[[Category: Scarsdale, J N]]

OCA at 11:37, 25 December 2014

2014-12-25T11:37:21Z

←Older revision		Revision as of 11:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8S FirstGlance]. <br>		<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8S FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [http://www.ebi.ac.uk/pdbsum/2a8s 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=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [http://www.ebi.ac.uk/pdbsum/2a8s PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NUD16_XENLA NUD16_XENLA]] RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms. The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP. Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions.<ref>PMID:15053875</ref> <ref>PMID:10585477</ref> <ref>PMID:17567574</ref> <ref>PMID:18820299</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Xenopus laevis]]		[[Category: Xenopus laevis]]
-	[[Category: Peculis, B A.]]	+	[[Category: Peculis, B A]]
-	[[Category: Scarsdale, J N.]]	+	[[Category: Scarsdale, J N]]
-	[[Category: Wright, H T.]]	+	[[Category: Wright, H T]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Modified nudix hydrolase fold]]		[[Category: Modified nudix hydrolase fold]]
	[[Category: Translation]]		[[Category: Translation]]

OCA at 00:35, 30 September 2014

2014-09-30T00:35:30Z

←Older revision		Revision as of 00:35, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2a8s.~~png~~\|~~left~~\|200px]]	+	==2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP==
		+	<StructureSection load='2a8s' size='340' side='right' caption='[[2a8s]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A8S FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=YCM:S-(2-AMINO-2-OXOETHYL)-L-CYSTEINE'>YCM</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u20\|1u20]], [[2a8p\|2a8p]], [[2a8q\|2a8q]], [[2a8r\|2a8r]], [[2a8t\|2a8t]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a8s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2a8s RCSB], [http://www.ebi.ac.uk/pdbsum/2a8s 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/a8/2a8s_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 ==
		+	X29, a 25 kDa Nudix hydrolase from Xenopus laevis that cleaves 5' caps from U8 snoRNA, crystallizes as a homodimeric apoenzyme. Manganese binds crystals of apo-X29 to form holo-X29 only in the presence of nucleot(s)ide. Structural changes in X29 on nucleo-t(s)ide-assisted Mn(+2) uptake account for the observed cooperativity of metal binding. Structures of X29 with GTP or m7GpppA show a different mode of ligand binding from that of other cap binding proteins and suggest a possible three- or four-metal Nudix reaction mechanism. The X29 dimer has no known RNA binding motif, but its striking surface dipolarity and unique structural features create a plausible RNA binding channel on the positive face of the protein. Because U8 snoRNP is essential for accumulation of mature 5.8S and 28S rRNA in vertebrate ribosome biogenesis, and cap structures are required for U8 stability in vivo, X29 could profoundly influence this fundamental cellular pathway.

-	~~{{STRUCTURE_2a8s\| PDB=2a8s \| SCENE= }}~~	+	Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes.,Scarsdale JN, Peculis BA, Wright HT Structure. 2006 Feb;14(2):331-43. PMID:16472752<ref>PMID:16472752</ref>

-	~~===2.45 Angstrom Crystal Structure~~ of the ~~Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16472752}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2a8s]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Xenopus_laevis Xenopus laevis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016472752<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Xenopus laevis]]		[[Category: Xenopus laevis]]
	[[Category: Peculis, B A.]]		[[Category: Peculis, B A.]]

OCA: Protected "2a8s" [edit=sysop:move=sysop]

2013-01-06T09:57:34Z

Protected "2a8s" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:57, 6 January 2013

OCA at 09:57, 6 January 2013

2013-01-06T09:57:31Z

←Older revision		Revision as of 09:57, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2a8s.png\|left\|200px]]		[[Image:2a8s.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2a8s\| PDB=2a8s \| SCENE= }}		{{STRUCTURE_2a8s\| PDB=2a8s \| SCENE= }}

	===2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP===		===2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and GTP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16472752}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16472752 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_16472752}}		{{ABSTRACT_PUBMED_16472752}}

	==About this Structure==		==About this Structure==
-	~~2A8S~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA].	+	[[2a8s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A8S OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16472752~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016472752</ref><references group="xtra"/>
	[[Category: Xenopus laevis]]		[[Category: Xenopus laevis]]
	[[Category: Peculis, B A.]]		[[Category: Peculis, B A.]]
	[[Category: Scarsdale, J N.]]		[[Category: Scarsdale, J N.]]
	[[Category: Wright, H T.]]		[[Category: Wright, H T.]]
		+	[[Category: Hydrolase]]
	[[Category: Modified nudix hydrolase fold]]		[[Category: Modified nudix hydrolase fold]]
-		+	[[Category: Translation]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 15:14:00 2009''~~	+