3bbd - Revision history

OCA at 05:41, 17 October 2024

2024-10-17T05:41:59Z

← Older revision		Revision as of 05:41, 17 October 2024
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	<StructureSection load='3bbd' size='340' side='right'caption='[[3bbd]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3bbd' size='340' side='right'caption='[[3bbd]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BBD 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>~~, ~~<scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.15Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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;~~'>~~[[3bbe\|3bbe]], [[3bbh\|3bbh]]~~</~~div~~>~~</td></tr>~~
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nep1 ([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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [https://pdbe.org/3bbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [https://www.ebi.ac.uk/pdbsum/3bbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbd 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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [https://pdbe.org/3bbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [https://www.ebi.ac.uk/pdbsum/3bbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NEP1_METJA NEP1_METJA]] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.<ref>PMID:20047967</ref>		[https://www.uniprot.org/uniprot/NEP1_METJA NEP1_METJA] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.<ref>PMID:20047967</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bb/3bbd_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bb/3bbd_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
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	==See Also==		==See Also==
	*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]		*[[Ribosome biogenesis protein 3D structures\|Ribosome biogenesis protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Atcc 43067]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Entian, K D]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Hart~~, P J~~]]		[[Category: Entian K-D]]
	[[Category: Kotter, P]]		[[Category: Hart PJ]]
	[[Category: Leal~~, B Z~~]]		[[Category: Kotter P]]
	[[Category: Meyer, B]]		[[Category: Leal BZ]]
	[[Category: Taylor~~, A B~~]]		[[Category: Meyer B]]
	[[Category: Wohnert, J]]		[[Category: Taylor AB]]
	~~[[Category: Methyltransferase]]~~		[[Category: Wohnert J]]
	~~[[Category: Ribosome biogenesis]]~~
	~~[[Category: Rrna processing]]~~
	~~[[Category: S-adenosyl-homocysteine]]~~
	~~[[Category: S-adenosyl-methionine]]~~
	~~[[Category: Transferase~~]]

OCA at 11:30, 5 January 2022

2022-01-05T11:30:18Z

← Older revision		Revision as of 11:30, 5 January 2022
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	==M. jannaschii Nep1 complexed with S-adenosyl-homocysteine==		==M. jannaschii Nep1 complexed with S-adenosyl-homocysteine==
	<StructureSection load='3bbd' size='340' side='right' caption='[[3bbd]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3bbd' size='340' side='right'caption='[[3bbd]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BBD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bbe\|3bbe]], [[3bbh\|3bbh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3bbe\|3bbe]], [[3bbh\|3bbh]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nep1 ([~~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">Nep1 ([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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [~~http~~://pdbe.org/3bbd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bbd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbd 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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [https://pdbe.org/3bbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [https://www.ebi.ac.uk/pdbsum/3bbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/NEP1_METJA NEP1_METJA]] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.<ref>PMID:20047967</ref>		[[https://www.uniprot.org/uniprot/NEP1_METJA NEP1_METJA]] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.<ref>PMID:20047967</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 43067]]		[[Category: Atcc 43067]]
			[[Category: Large Structures]]
	[[Category: Entian, K D]]		[[Category: Entian, K D]]
	[[Category: Hart, P J]]		[[Category: Hart, P J]]

OCA at 07:58, 31 October 2018

2018-10-31T07:58:29Z

← Older revision		Revision as of 07:58, 31 October 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/bb/3bbd_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bb/3bbd_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3bbd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3bbd" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Ribosome biogenesis protein\|Ribosome biogenesis protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:53, 4 August 2016

2016-08-04T21:53:22Z

← Older revision		Revision as of 21:53, 4 August 2016
Line 1:		Line 1:

	==M. jannaschii Nep1 complexed with S-adenosyl-homocysteine==		==M. jannaschii Nep1 complexed with S-adenosyl-homocysteine==
	<StructureSection load='3bbd' size='340' side='right' caption='[[3bbd]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='3bbd' size='340' side='right' caption='[[3bbd]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BBD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bbe\|3bbe]], [[3bbh\|3bbh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bbe\|3bbe]], [[3bbh\|3bbh]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nep1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ~~Methanocaldococcus jannaschii~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nep1 ([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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [http://www.ebi.ac.uk/pdbsum/3bbd 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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [http://pdbe.org/3bbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [http://www.ebi.ac.uk/pdbsum/3bbd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bbd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3bbd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3bbd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Methanocaldococcus jannaschii~~]]		[[Category: Atcc 43067]]
	[[Category: Entian, K D]]		[[Category: Entian, K D]]
	[[Category: Hart, P J]]		[[Category: Hart, P J]]

OCA at 13:27, 25 December 2014

2014-12-25T13:27:23Z

← Older revision		Revision as of 13:27, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BBD FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bbe\|3bbe]], [[3bbh\|3bbh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bbe\|3bbe]], [[3bbh\|3bbh]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nep1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nep1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [http://www.ebi.ac.uk/pdbsum/3bbd 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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [http://www.ebi.ac.uk/pdbsum/3bbd PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/NEP1_METJA NEP1_METJA]] Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.<ref>PMID:20047967</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Entian, K D.]]		[[Category: Entian, K D]]
	[[Category: Hart, P J.]]		[[Category: Hart, P J]]
	[[Category: Kotter, P.]]		[[Category: Kotter, P]]
	[[Category: Leal, B Z.]]		[[Category: Leal, B Z]]
	[[Category: Meyer, B.]]		[[Category: Meyer, B]]
	[[Category: Taylor, A B.]]		[[Category: Taylor, A B]]
	[[Category: Wohnert, J.]]		[[Category: Wohnert, J]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Ribosome biogenesis]]		[[Category: Ribosome biogenesis]]

OCA at 21:13, 2 October 2014

2014-10-02T21:13:46Z

← Older revision		Revision as of 21:13, 2 October 2014
Line 1:		Line 1:
	[[Image:~~3bbd~~.~~png~~\|~~left~~\|~~200px~~]]		==M. jannaschii Nep1 complexed with S-adenosyl-homocysteine==
			<StructureSection load='3bbd' size='340' side='right' caption='[[3bbd]], [[Resolution\|resolution]] 2.15Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3bbd]] is a 2 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=3BBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BBD FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3bbe\|3bbe]], [[3bbh\|3bbh]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Nep1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</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=3bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bbd RCSB], [http://www.ebi.ac.uk/pdbsum/3bbd 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/bb/3bbd_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 ==
			Ribosome biogenesis in eukaryotes requires the participation of a large number of ribosome assembly factors. The highly conserved eukaryotic nucleolar protein Nep1 has an essential but unknown function in 18S rRNA processing and ribosome biogenesis. In Saccharomyces cerevisiae the malfunction of a temperature-sensitive Nep1 protein (nep1-1(ts)) was suppressed by the addition of S-adenosylmethionine (SAM). This suggests the participation of Nep1 in a methyltransferase reaction during ribosome biogenesis. In addition, yeast Nep1 binds to a 6-nt RNA-binding motif also found in 18S rRNA and facilitates the incorporation of ribosomal protein Rps19 during the formation of pre-ribosomes. Here, we present the X-ray structure of the Nep1 homolog from the archaebacterium Methanocaldococcus jannaschii in its free form (2.2 A resolution) and bound to the S-adenosylmethionine analog S-adenosylhomocysteine (SAH, 2.15 A resolution) and the antibiotic and general methyltransferase inhibitor sinefungin (2.25 A resolution). The structure reveals a fold which is very similar to the conserved core fold of the SPOUT-class methyltransferases but contains a novel extension of this common core fold. SAH and sinefungin bind to Nep1 at a preformed binding site that is topologically equivalent to the cofactor-binding site in other SPOUT-class methyltransferases. Therefore, our structures together with previous genetic data suggest that Nep1 is a genuine rRNA methyltransferase.

	~~{{STRUCTURE_3bbd\| PDB=3bbd \| SCENE= }}~~		The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.,Taylor AB, Meyer B, Leal BZ, Kotter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wohnert J Nucleic Acids Res. 2008 Mar;36(5):1542-54. Epub 2008 Jan 21. PMID:18208838<ref>PMID:18208838</ref>

	~~===M~~. ~~jannaschii Nep1 complexed with~~ S~~-adenosyl-homocysteine===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18208838}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3bbd]] is a 2 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=3BBD OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018208838<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Entian, K D.]]		[[Category: Entian, K D.]]

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

2013-01-07T20:53:30Z

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

← Older revision	Revision as of 20:53, 7 January 2013
(No difference)

OCA at 20:53, 7 January 2013

2013-01-07T20:53:28Z

← Older revision		Revision as of 20:53, 7 January 2013
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	~~{{Seed}}~~
	[[Image:3bbd.png\|left\|200px]]		[[Image:3bbd.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3bbd", 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_3bbd\| PDB=3bbd \| SCENE= }}		{{STRUCTURE_3bbd\| PDB=3bbd \| SCENE= }}

	===M. jannaschii Nep1 complexed with S-adenosyl-homocysteine===		===M. jannaschii Nep1 complexed with S-adenosyl-homocysteine===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18208838}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18208838 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18208838}}		{{ABSTRACT_PUBMED_18208838}}

	==About this Structure==		==About this Structure==
	~~3BBD~~ is a 2 ~~chains~~ structure ~~of sequences~~ 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=3BBD OCA].		[[3bbd]] is a 2 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=3BBD OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18208838~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018208838</ref><references group="xtra"/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Entian, K D.]]		[[Category: Entian, K D.]]
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	[[Category: S-adenosyl-homocysteine]]		[[Category: S-adenosyl-homocysteine]]
	[[Category: S-adenosyl-methionine]]		[[Category: S-adenosyl-methionine]]
			[[Category: Transferase]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 17:23:57 2009''~~

OCA at 15:23, 17 February 2009

2009-02-17T15:23:58Z

← Older revision		Revision as of 15:23, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	3BBD is a ~~[[Single protein]]~~ structure of ~~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=3BBD OCA].		3BBD is a 2 chains structure of sequences 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=3BBD OCA].

	==Reference==		==Reference==
	The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site., Taylor AB, Meyer B, Leal BZ, Kotter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wohnert J, Nucleic Acids Res. 2008 Mar;36(5):1542-54. Epub 2008 Jan 21. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18208838 18208838]~~		<ref group="xtra">PMID:18208838</ref><references group="xtra"/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	~~[[Category: Single protein]]~~
	[[Category: Entian, K D.]]		[[Category: Entian, K D.]]
	[[Category: Hart, P J.]]		[[Category: Hart, P J.]]
Line 39:		Line 38:
	[[Category: S-adenosyl-methionine]]		[[Category: S-adenosyl-methionine]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:21:~~41 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:23:57 2009''

OCA at 21:21, 28 July 2008

2008-07-28T21:21:46Z

← Older revision		Revision as of 21:21, 28 July 2008
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	[[Image:3bbd.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:3bbd.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3bbd\| PDB=3bbd \| SCENE= }}		{{STRUCTURE_3bbd\| PDB=3bbd \| SCENE= }}

	~~'''~~M. jannaschii Nep1 complexed with S-adenosyl-homocysteine~~'''~~		===M. jannaschii Nep1 complexed with S-adenosyl-homocysteine===


	~~==Overview==~~		<!--
	~~Ribosome biogenesis in eukaryotes requires the participation of a large number of ribosome assembly factors.~~ The highly conserved eukaryotic nucleolar protein Nep1 has an essential but unknown function in 18S rRNA processing and ribosome biogenesis. In Saccharomyces cerevisiae the malfunction of a temperature-sensitive Nep1 protein (nep1-1(ts)) was suppressed by the addition of S-adenosylmethionine (SAM). This suggests the participation of Nep1 in a methyltransferase reaction during ribosome biogenesis. In addition, ~~yeast Nep1 binds to a 6-nt RNA-binding motif also found in 18S rRNA and facilitates the incorporation of ribosomal protein Rps19 during the formation of pre-ribosomes. Here~~, ~~we present~~ the ~~X-ray structure of the Nep1 homolog from the archaebacterium Methanocaldococcus jannaschii in its free form (2.2 A resolution) and bound~~ to the ~~S-adenosylmethionine analog S-adenosylhomocysteine~~ (~~SAH, 2~~.~~15 A resolution) and the antibiotic and general methyltransferase inhibitor sinefungin (2~~.~~25 A resolution~~)~~. The structure reveals a fold which~~ is ~~very similar to~~ the ~~conserved core fold of the SPOUT-class methyltransferases but contains a novel extension of this common core fold~~. ~~SAH and sinefungin bind to Nep1 at a preformed binding site that is topologically equivalent to the cofactor~~-~~binding site in other SPOUT~~-~~class methyltransferases. Therefore, our structures together with previous genetic data suggest that Nep1 is a genuine rRNA methyltransferase.~~		The line below this paragraph, {{ABSTRACT_PUBMED_18208838}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 18208838 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_18208838}}

	==About this Structure==		==About this Structure==
Line 34:		Line 38:
	[[Category: S-adenosyl-homocysteine]]		[[Category: S-adenosyl-homocysteine]]
	[[Category: S-adenosyl-methionine]]		[[Category: S-adenosyl-methionine]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Apr 30 13~~:36:56 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 00:21:41 2008''