3gru - Revision history

OCA at 07:11, 6 September 2023

OCA — Wed, 06 Sep 2023 07:11:27 GMT

←Older revision		Revision as of 07:11, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3gru' size='340' side='right'caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3gru' size='340' side='right'caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43067 Atcc 43067~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GRU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">ksgA, MJ1029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])~~</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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [https://pdbe.org/3gru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [https://www.ebi.ac.uk/pdbsum/3gru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gru 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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [https://pdbe.org/3gru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [https://www.ebi.ac.uk/pdbsum/3gru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gru ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>	+	[https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43067]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Musayev, F N~~]]	+	[[Category: Methanocaldococcus jannaschii]]
-	[[Category: ~~Rife, J P~~]]	+	[[Category: Musayev FN]]
-	[[Category: ~~Scarsdale, J N~~]]	+	[[Category: Rife JP]]
-	[[Category: ~~Dimethyladenosine transferase]]~~	+	[[Category: Scarsdale JN]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Ribosomal assembly s-adenosyl-l-methionine]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Rossmann fold]]~~	+
-	~~[[Category: Rrna]]~~	+
-	~~[[Category: Rrna processing]]~~	+
-	~~[[Category: S-adenosyl-l-methionine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 20:09, 20 October 2021

OCA — Wed, 20 Oct 2021 20:09:45 GMT

←Older revision		Revision as of 20:09, 20 October 2021
Line 1:		Line 1:

	==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1==		==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1==
-	<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3gru' size='340' side='right'caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GRU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [~~http~~://pdbe.org/3gru PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gru PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gru 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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [https://pdbe.org/3gru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [https://www.ebi.ac.uk/pdbsum/3gru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gru ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>	+	[[https://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Adenosine dimethyltransferase\|Adenosine dimethyltransferase]]	+	*[[Adenosine dimethyltransferase 3D structures\|Adenosine dimethyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43067]]		[[Category: Atcc 43067]]
		+	[[Category: Large Structures]]
	[[Category: Musayev, F N]]		[[Category: Musayev, F N]]
	[[Category: Rife, J P]]		[[Category: Rife, J P]]

OCA at 05:28, 7 December 2018

OCA — Fri, 07 Dec 2018 05:28:55 GMT

←Older revision		Revision as of 05:28, 7 December 2018
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gr/3gru_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gr/3gru_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 12:08, 5 August 2016

OCA — Fri, 05 Aug 2016 12:08:49 GMT

←Older revision		Revision as of 12:08, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1==		==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1==
	<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru 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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://pdbe.org/3gru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gru ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		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=3gru ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		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 3gru" style="background-color:#fffaf0;"></div>

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

OCA at 02:19, 25 December 2014

OCA — Thu, 25 Dec 2014 02:19:04 GMT

←Older revision		Revision as of 02:19, 25 December 2014
Line 2:		Line 2:
	<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GRU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru 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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RSMA_METJA RSMA_METJA]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits.[HAMAP-Rule:MF_00607]<ref>PMID:19520088</ref> <ref>PMID:20163168</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43067]]
	[[Category: Musayev, F N]]		[[Category: Musayev, F N]]
	[[Category: Rife, J P]]		[[Category: Rife, J P]]

OCA at 07:24, 12 November 2014

OCA — Wed, 12 Nov 2014 07:24:05 GMT

←Older revision		Revision as of 07:24, 12 November 2014
Line 2:		Line 2:
	<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GRU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru 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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru PDBsum]</span></td></tr>
	</table>		</table>
Line 33:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Methanocaldococcus jannaschii]]~~	+	[[Category: Musayev, F N]]
-	[[Category: Musayev, F N.]]	+	[[Category: Rife, J P]]
-	[[Category: Rife, J P.]]	+	[[Category: Scarsdale, J N]]
-	[[Category: Scarsdale, J N.]]	+
	[[Category: Dimethyladenosine transferase]]		[[Category: Dimethyladenosine transferase]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]

OCA at 14:18, 3 November 2014

OCA — Mon, 03 Nov 2014 14:18:57 GMT

←Older revision		Revision as of 14:18, 3 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3gru.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1==
		+	<StructureSection load='3gru' size='340' side='right' caption='[[3gru]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gru]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GRU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fyc\|3fyc]], [[3fyd\|3fyd]], [[1qyr\|1qyr]], [[2h1r\|2h1r]], [[1zq9\|1zq9]], [[3fuv\|3fuv]], [[3fut\|3fut]], [[3fuu\|3fuu]], [[3fux\|3fux]], [[3fuw\|3fuw]], [[3grr\|3grr]], [[3grv\|3grv]], [[3gry\|3gry]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ksgA, MJ1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3gru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gru RCSB], [http://www.ebi.ac.uk/pdbsum/3gru 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/gr/3gru_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 KsgA/Dim1 family of proteins is intimately involved in ribosome biogenesis in all organisms. These enzymes share the common function of dimethylating two adenosine residues near the 3'-OH end of the small subunit rRNA; orthologs in the three kingdoms, along with eukaryotic organelles, have evolved additional functions in rRNA processing, ribosome assembly, and, surprisingly, transcription in mitochondria. The methyltransferase reaction is intriguingly elaborate. The enzymes can bind to naked small subunit rRNA but cannot methylate their target bases until a subset of ribosomal proteins have bound and the nascent subunit has reached a certain level of maturity. Once this threshold is reached, the enzyme must stabilize two adenosines into the active site at separate times and two methyl groups must be transferred to each adenosine, with concomitant exchanges of the product S-adenosyl-l-homocysteine and the methyl donor substrate S-adenosyl-l-methionine. A detailed molecular understanding of this mechanism is currently lacking. Structural analysis of the interactions between the enzyme and substrate will aid in this understanding. Here we present the structure of KsgA from Methanocaldococcus jannaschii in complex with several ligands, including the first structure of S-adenosyl-l-methionine bound to a KsgA/Dim1 enzyme in a catalytically productive way. We also discuss the inability thus far to determine a structure of a target adenosine bound in its active site.

-	~~{{STRUCTURE_3gru\| PDB=3gru \| SCENE= }}~~	+	Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design.,O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP Biochemistry. 2010 Mar 30;49(12):2697-704. PMID:20163168<ref>PMID:20163168</ref>

-	~~===Crystal Structure~~ of the ~~Complex between AMP and Methanocaldococcus jannaschi Dim1===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_20163168}}~~	+	==See Also==
-		+	*[[Adenosine dimethyltransferase\|Adenosine dimethyltransferase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3gru~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:020163168<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Musayev, F N.]]		[[Category: Musayev, F N.]]
Line 20:		Line 41:
	[[Category: Ribosomal assembly s-adenosyl-l-methionine]]		[[Category: Ribosomal assembly s-adenosyl-l-methionine]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
-	[[Category: ~~Rossman~~ fold]]	+	[[Category: Rossmann fold]]
	[[Category: Rrna]]		[[Category: Rrna]]
	[[Category: Rrna processing]]		[[Category: Rrna processing]]
	[[Category: S-adenosyl-l-methionine]]		[[Category: S-adenosyl-l-methionine]]
	[[Category: Transferase]]		[[Category: Transferase]]

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

OCA — Wed, 27 Feb 2013 15:35:55 GMT

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

←Older revision

Revision as of 15:35, 27 February 2013

OCA at 15:35, 27 February 2013

OCA — Wed, 27 Feb 2013 15:35:53 GMT

←Older revision		Revision as of 15:35, 27 February 2013
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-	{{Seed}}
	[[Image:3gru.png\|left\|200px]]		[[Image:3gru.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gru", 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_3gru\| PDB=3gru \| SCENE= }}		{{STRUCTURE_3gru\| PDB=3gru \| SCENE= }}

	===Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1===		===Crystal Structure of the Complex between AMP and Methanocaldococcus jannaschi Dim1===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20163168}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20163168 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_20163168}}		{{ABSTRACT_PUBMED_20163168}}

	==About this Structure==		==About this Structure==
-	~~3GRU~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA].	+	[[3gru]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GRU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20163168~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020163168</ref><references group="xtra"/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Musayev, F N.]]		[[Category: Musayev, F N.]]
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	[[Category: S-adenosyl-l-methionine]]		[[Category: S-adenosyl-l-methionine]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 7 10:05:06 2010''

OCA at 07:05, 7 April 2010

OCA — Wed, 07 Apr 2010 07:05:06 GMT

←Older revision		Revision as of 07:05, 7 April 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3gru.~~jpg~~\|left\|200px]]	+	[[Image:3gru.png\|left\|200px]]

	<!--		<!--
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	[[Category: Transferase]]		[[Category: Transferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 31 13~~:37:53 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 7 10:05:06 2010''