1u20 - Revision history

OCA at 08:43, 14 February 2024

2024-02-14T08:43:37Z

←Older revision		Revision as of 08:43, 14 February 2024
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	<StructureSection load='1u20' size='340' side='right'caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u20' size='340' side='right'caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U20 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U20 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></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]] 2.1Å</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></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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [https://pdbe.org/1u20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [https://www.ebi.ac.uk/pdbsum/1u20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u20 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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [https://pdbe.org/1u20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [https://www.ebi.ac.uk/pdbsum/1u20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u20 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]]
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	__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~~]]	+

OCA at 09:35, 29 September 2021

2021-09-29T09:35:27Z

←Older revision		Revision as of 09:35, 29 September 2021
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	<StructureSection load='1u20' size='340' side='right'caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u20' size='340' side='right'caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1U20 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U20 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></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></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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [~~http~~://pdbe.org/1u20 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1u20 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1u20 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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [https://pdbe.org/1u20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [https://www.ebi.ac.uk/pdbsum/1u20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u20 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 13:54, 25 December 2019

2019-12-25T13:54:56Z

←Older revision		Revision as of 13:54, 25 December 2019
Line 1:		Line 1:

	==Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29==		==Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29==
-	<StructureSection load='1u20' size='340' side='right' caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1u20' size='340' side='right'caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 FirstGlance]. <br>
Line 24:		Line 24:
	</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 08:44, 21 March 2018

2018-03-21T08:44:34Z

←Older revision		Revision as of 08:44, 21 March 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29==		==Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29==
	<StructureSection load='1u20' size='340' side='right' caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u20' size='340' side='right' caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 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></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></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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [http://pdbe.org/1u20 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [http://www.ebi.ac.uk/pdbsum/1u20 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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [http://pdbe.org/1u20 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [http://www.ebi.ac.uk/pdbsum/1u20 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u20 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u2/1u20_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u2/1u20_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 13:17, 8 February 2016

2016-02-08T13:17:10Z

←Older revision		Revision as of 13:17, 8 February 2016
Line 16:		Line 16:
	<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=1u20 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	== References ==		== References ==

OCA at 11:56, 10 September 2015

2015-09-10T11:56:24Z

←Older revision		Revision as of 11:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1u20' size='340' side='right' caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1u20' size='340' side='right' caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 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></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></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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [http://www.ebi.ac.uk/pdbsum/1u20 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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [http://pdbe.org/1u20 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [http://www.ebi.ac.uk/pdbsum/1u20 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 16:		Line 18:
	</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/chain_selection.php?pdb_ID=2ata ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	== 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 12:47, 6 January 2015

2015-01-06T12:47:12Z

←Older revision		Revision as of 12:47, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [http://www.ebi.ac.uk/pdbsum/1u20 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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [http://www.ebi.ac.uk/pdbsum/1u20 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</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]]

OCA at 19:34, 29 September 2014

2014-09-29T19:34:36Z

←Older revision		Revision as of 19:34, 29 September 2014
Line 1:		Line 1:
-	~~[[Image:1u20.png\|left\|200px]]~~	+	==Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29==
-		+	<StructureSection load='1u20' size='340' side='right' caption='[[1u20]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{STRUCTURE_1u20\| PDB=1u20 \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[1u20]] 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=1U20 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U20 FirstGlance]. <br>
-	===Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29===	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
-		+	<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=1u20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u20 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u20 RCSB], [http://www.ebi.ac.uk/pdbsum/1u20 PDBsum]</span></td></tr>
-	~~{{ABSTRACT_PUBMED_016472752}}~~	+	<table>
-		+	== Evolutionary Conservation ==
-	==~~About this Structure~~==	+	[[Image:Consurf_key_small.gif\|200px\|right]]
-	[[1u20]] 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=1U20 OCA].	+	Check<jmol>
-		+	<jmolCheckbox>
-	==~~Reference~~==	+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u2/1u20_consurf.spt"</scriptWhenChecked>
-	<~~ref group~~="~~xtra~~">~~PMID~~:~~016472752~~</~~ref~~><~~references group~~="~~xtra~~"/>	+	<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>
		+	__TOC__
		+	</StructureSection>
	[[Category: Xenopus laevis]]		[[Category: Xenopus laevis]]
	[[Category: Peculis, B A.]]		[[Category: Peculis, B A.]]

OCA: Protected "1u20" [edit=sysop:move=sysop]

2013-01-05T12:45:01Z

Protected "1u20" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:45, 5 January 2013

OCA at 12:44, 5 January 2013

2013-01-05T12:44:56Z

←Older revision		Revision as of 12:44, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1u20.png\|left\|200px]]		[[Image:1u20.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1u20", 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_1u20\| PDB=1u20 \| SCENE= }}		{{STRUCTURE_1u20\| PDB=1u20 \| SCENE= }}

	===Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29===		===Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29===

		+	{{ABSTRACT_PUBMED_016472752}}

	==About this Structure==		==About this Structure==
-	~~1U20~~ 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=1U20 OCA].	+	[[1u20]] 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=1U20 OCA].
		+
		+	==Reference==
		+	<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]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:22:18 2009''