3g96 - Revision history

OCA at 09:53, 21 February 2024

OCA — Wed, 21 Feb 2024 09:53:07 GMT

←Older revision		Revision as of 09:53, 21 February 2024
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	<StructureSection load='3g96' size='340' side='right'caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='3g96' size='340' side='right'caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G96 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=6MN:2~~-~~AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3.01Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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;~~'>~~[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [https://pdbe.org/3g96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [https://www.ebi.ac.uk/pdbsum/3g96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g96 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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [https://pdbe.org/3g96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [https://www.ebi.ac.uk/pdbsum/3g96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g96 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>	+	[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3g96 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=3g96 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, much of the structural work to date has been done on a variant glmS ribozyme, derived from Thermoanaerobacter tengcongensis. Here we present structures of the B. anthracis glmS ribozyme in states before the activating sugar, glucosamine 6-phosphate (GlcN6P), has bound and after the reaction has occurred. These structures show an active site preorganized to bind GlcN6P that retains some affinity for the sugar even after cleavage of the RNA backbone. A structure of an inactive glmS ribozyme with a mutation distal from the ligand-binding pocket highlights a nucleotide critical to the reaction that does not affect GlcN6P binding. Structures of the glmS ribozyme bound to a naturally occurring inhibitor, glucose 6-phosphate (Glc6P), and a nonnatural activating sugar, mannosamine 6-phosphate (MaN6P), reveal a binding mode similar to that of GlcN6P. Kinetic analyses show a pH dependence of ligand binding that is consistent with titration of the cofactor's phosphate group and support a model in which the major determinant of activity is the sugar amine independent of its stereochemical presentation.
-
-	Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme.,Cochrane JC, Lipchock SV, Smith KD, Strobel SA Biochemistry. 2009 Apr 21;48(15):3239-46. PMID:19228039<ref>PMID:19228039</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3g96" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]		*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Cochrane, J C~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Lipchock, S V~~]]	+	[[Category: Cochrane JC]]
-	[[Category: ~~Smith, K D~~]]	+	[[Category: Lipchock SV]]
-	[[Category: ~~Strobel, S A~~]]	+	[[Category: Smith KD]]
-	[[Category: ~~Catalytic rna]]~~	+	[[Category: Strobel SA]]
-	~~[[Category: Rna binding protein-rna complex~~]]	+

OCA at 20:03, 20 October 2021

OCA — Wed, 20 Oct 2021 20:03:41 GMT

←Older revision		Revision as of 20:03, 20 October 2021
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	==Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P==		==Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P==
-	<StructureSection load='3g96' size='340' side='right' caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>	+	<StructureSection load='3g96' size='340' side='right'caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G96 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</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=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [~~http~~://pdbe.org/3g96 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g96 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g96 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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [https://pdbe.org/3g96 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [https://www.ebi.ac.uk/pdbsum/3g96 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g96 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>	+	[[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Nucleoprotein\|Nucleoprotein]]	+	*[[Nucleoprotein 3D structures\|Nucleoprotein 3D structures]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cochrane, J C]]		[[Category: Cochrane, J C]]
	[[Category: Lipchock, S V]]		[[Category: Lipchock, S V]]

OCA at 06:32, 4 April 2018

OCA — Wed, 04 Apr 2018 06:32:02 GMT

←Older revision		Revision as of 06:32, 4 April 2018
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	==See Also==		==See Also==
		+	*[[Nucleoprotein\|Nucleoprotein]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==

OCA at 06:32, 7 February 2018

OCA — Wed, 07 Feb 2018 06:32:20 GMT

←Older revision		Revision as of 06:32, 7 February 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g9/3g96_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g9/3g96_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 07:00, 1 November 2017

OCA — Wed, 01 Nov 2017 07:00:26 GMT

←Older revision		Revision as of 07:00, 1 November 2017
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		+
	==Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P==		==Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P==
	<StructureSection load='3g96' size='340' side='right' caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='3g96' size='340' side='right' caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [http://pdbe.org/3g96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [http://www.ebi.ac.uk/pdbsum/3g96 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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [http://pdbe.org/3g96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [http://www.ebi.ac.uk/pdbsum/3g96 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g96 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	==See Also==		==See Also==
-	*[[Nucleoprotein\|Nucleoprotein]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==

OCA at 05:42, 10 February 2016

OCA — Wed, 10 Feb 2016 05:42:15 GMT

←Older revision		Revision as of 05:42, 10 February 2016
Line 2:		Line 2:
	<StructureSection load='3g96' size='340' side='right' caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='3g96' size='340' side='right' caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G96 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G96 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</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=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [http://www.ebi.ac.uk/pdbsum/3g96 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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [http://pdbe.org/3g96 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [http://www.ebi.ac.uk/pdbsum/3g96 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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=3g96 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3g96" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cochrane, J C]]		[[Category: Cochrane, J C]]
	[[Category: Lipchock, S V]]		[[Category: Lipchock, S V]]

OCA at 12:12, 25 December 2014

OCA — Thu, 25 Dec 2014 12:12:17 GMT

←Older revision		Revision as of 12:12, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G96 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G96 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [http://www.ebi.ac.uk/pdbsum/3g96 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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [http://www.ebi.ac.uk/pdbsum/3g96 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cochrane, J C.]]	+	[[Category: Cochrane, J C]]
-	[[Category: Lipchock, S V.]]	+	[[Category: Lipchock, S V]]
-	[[Category: Smith, K D.]]	+	[[Category: Smith, K D]]
-	[[Category: Strobel, S A.]]	+	[[Category: Strobel, S A]]
	[[Category: Catalytic rna]]		[[Category: Catalytic rna]]
	[[Category: Rna binding protein-rna complex]]		[[Category: Rna binding protein-rna complex]]

OCA at 12:08, 29 September 2014

OCA — Mon, 29 Sep 2014 12:08:13 GMT

←Older revision		Revision as of 12:08, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3g96.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of the Bacillus anthracis glmS ribozyme bound to MaN6P==
		+	<StructureSection load='3g96' size='340' side='right' caption='[[3g96]], [[Resolution\|resolution]] 3.01Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g96]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G96 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MN:2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE'>6MN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g8s\|3g8s]], [[3g8t\|3g8t]], [[3g95\|3g95]], [[3g9c\|3g9c]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3g96 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g96 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g96 RCSB], [http://www.ebi.ac.uk/pdbsum/3g96 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/g9/3g96_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 glmS ribozyme is the first naturally occurring catalytic RNA that relies on an exogenous, nonnucleotide cofactor for reactivity. From a biochemical perspective, the glmS ribozyme derived from Bacillus anthracis is the best characterized. However, much of the structural work to date has been done on a variant glmS ribozyme, derived from Thermoanaerobacter tengcongensis. Here we present structures of the B. anthracis glmS ribozyme in states before the activating sugar, glucosamine 6-phosphate (GlcN6P), has bound and after the reaction has occurred. These structures show an active site preorganized to bind GlcN6P that retains some affinity for the sugar even after cleavage of the RNA backbone. A structure of an inactive glmS ribozyme with a mutation distal from the ligand-binding pocket highlights a nucleotide critical to the reaction that does not affect GlcN6P binding. Structures of the glmS ribozyme bound to a naturally occurring inhibitor, glucose 6-phosphate (Glc6P), and a nonnatural activating sugar, mannosamine 6-phosphate (MaN6P), reveal a binding mode similar to that of GlcN6P. Kinetic analyses show a pH dependence of ligand binding that is consistent with titration of the cofactor's phosphate group and support a model in which the major determinant of activity is the sugar amine independent of its stereochemical presentation.

-	~~{{STRUCTURE_3g96\| PDB=3g96 \| SCENE= }}~~	+	Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme.,Cochrane JC, Lipchock SV, Smith KD, Strobel SA Biochemistry. 2009 Apr 21;48(15):3239-46. PMID:19228039<ref>PMID:19228039</ref>

-	~~===Crystal structure~~ of the ~~Bacillus anthracis glmS ribozyme bound to MaN6P===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19228039}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3g96]] is a 12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoprotein\|Nucleoprotein]]		*[[Nucleoprotein\|Nucleoprotein]]
	*[[Ribozyme\|Ribozyme]]		*[[Ribozyme\|Ribozyme]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019228039<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Cochrane, J C.]]		[[Category: Cochrane, J C.]]

OCA at 16:31, 20 October 2012

OCA — Sat, 20 Oct 2012 16:31:25 GMT

←Older revision		Revision as of 16:31, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3g96]] is a 12 chain structure ~~of [[Nucleoprotein]] and [[Ribozyme]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA].	+	[[3g96]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G96 OCA].

	==See Also==		==See Also==

OCA: Protected "3g96" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 21:57:32 GMT

Protected "3g96" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:57, 26 July 2012