3oin - Revision history

OCA at 09:40, 6 September 2023

OCA — Wed, 06 Sep 2023 09:40:06 GMT

←Older revision		Revision as of 09:40, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3oin' size='340' side='right'caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3oin' size='340' side='right'caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OIN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.9Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</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;'>[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</div></td></tr>	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [https://pdbe.org/3oin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [https://www.ebi.ac.uk/pdbsum/3oin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oin 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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [https://pdbe.org/3oin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [https://www.ebi.ac.uk/pdbsum/3oin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oin ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref>	+	[https://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~RRNA small subunit pseudouridine methyltransferase Nep1~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: LaRonde-LeBlanc, N]]	+	[[Category: LaRonde-LeBlanc N]]
-	[[Category: Thomas~~, S R]]~~	+	[[Category: Thomas SR]]
-	~~[[Category: Emg1]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Ribosomal protein]]~~	+
-	~~[[Category: Ribosome biogenesis]]~~	+
-	~~[[Category: Rrna processing]]~~	+
-	~~[[Category: Scnep1]]~~	+
-	~~[[Category: Spout~~]]	+

OCA at 10:44, 18 May 2022

OCA — Wed, 18 May 2022 10:44:52 GMT

OCA at 05:52, 22 April 2020

OCA — Wed, 22 Apr 2020 05:52:00 GMT

←Older revision		Revision as of 05:52, 22 April 2020
Line 1:		Line 1:

-	==Crystal structure of Saccharomyces ~~Cerevisiae~~ Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA==	+	==Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA==
-	<StructureSection load='3oin' size='340' side='right' caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3oin' size='340' side='right'caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3OIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3OIN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [http://pdbe.org/3oin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [http://www.ebi.ac.uk/pdbsum/3oin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3oin ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [http://pdbe.org/3oin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [http://www.ebi.ac.uk/pdbsum/3oin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3oin ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
		+	[[Category: RRNA small subunit pseudouridine methyltransferase Nep1]]
	[[Category: LaRonde-LeBlanc, N]]		[[Category: LaRonde-LeBlanc, N]]
	[[Category: Thomas, S R]]		[[Category: Thomas, S R]]

OCA at 11:41, 4 August 2016

OCA — Thu, 04 Aug 2016 11:41:16 GMT

←Older revision		Revision as of 11:41, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA==		==Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA==
	<StructureSection load='3oin' size='340' side='right' caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3oin' size='340' side='right' caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OIN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [http://www.ebi.ac.uk/pdbsum/3oin 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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [http://pdbe.org/3oin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [http://www.ebi.ac.uk/pdbsum/3oin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3oin ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~EMG1_YEAST EMG1_YEAST~~]] ~~Has an essential role in 40S ribosomal subunit biogenesis and 18S rRNA processing. Probably catalyzes the N1~~-~~methylation of~~ pseudouridine at position 1189 (Psi1189) in 18S rRNA. ~~Thus, is most likely the methyltransferase involved in~~ the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in ~~position 1189 in~~ 18S rRNA. Is also ~~involved~~ in ~~ribosome assembly~~.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:21087996</ref>	+	[[http://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	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 3oin" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: LaRonde-LeBlanc, N]]		[[Category: LaRonde-LeBlanc, N]]
	[[Category: Thomas, S R]]		[[Category: Thomas, S R]]

OCA at 08:57, 25 December 2014

OCA — Thu, 25 Dec 2014 08:57:01 GMT

←Older revision		Revision as of 08:57, 25 December 2014
Line 8:		Line 8:
	<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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [http://www.ebi.ac.uk/pdbsum/3oin 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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [http://www.ebi.ac.uk/pdbsum/3oin PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/EMG1_YEAST EMG1_YEAST]] Has an essential role in 40S ribosomal subunit biogenesis and 18S rRNA processing. Probably catalyzes the N1-methylation of pseudouridine at position 1189 (Psi1189) in 18S rRNA. Thus, is most likely the methyltransferase involved in the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in position 1189 in 18S rRNA. Is also involved in ribosome assembly.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:21087996</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:11, 19 December 2014

OCA — Fri, 19 Dec 2014 07:11:03 GMT

←Older revision		Revision as of 07:11, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3oin\| PDB=3oin \| SCENE= }}~~	+	==Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA==
-	===Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA===	+	<StructureSection load='3oin' size='340' side='right' caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21087996}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OIN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [http://www.ebi.ac.uk/pdbsum/3oin PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen-Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase.

-	~~==About this Structure==~~	+	Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.,Thomas SR, Keller CA, Szyk A, Cannon JR, Laronde-Leblanc NA Nucleic Acids Res. 2010 Nov 17. PMID:21087996<ref>PMID:21087996</ref>
-	~~[[3oin]] is a 3 chain structure with sequence from [http:~~/~~/en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:021087996</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: LaRonde-LeBlanc, N.]]	+	[[Category: LaRonde-LeBlanc, N]]
-	[[Category: Thomas, S R.]]	+	[[Category: Thomas, S R]]
	[[Category: Emg1]]		[[Category: Emg1]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]

OCA at 08:23, 2 May 2013

OCA — Thu, 02 May 2013 08:23:02 GMT

←Older revision		Revision as of 08:23, 2 May 2013
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-	[[Image:3oin.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3oin", creates the "Structure Box" on the page.
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-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-	-->
	{{STRUCTURE_3oin\| PDB=3oin \| SCENE= }}		{{STRUCTURE_3oin\| PDB=3oin \| SCENE= }}
-
	===Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA===		===Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21087996}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21087996 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_21087996}}		{{ABSTRACT_PUBMED_21087996}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21087996~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021087996</ref><references group="xtra"/><references/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: LaRonde-LeBlanc, N.]]		[[Category: LaRonde-LeBlanc, N.]]
	[[Category: Thomas, S R.]]		[[Category: Thomas, S R.]]
		+	[[Category: Emg1]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Ribosomal protein]]
		+	[[Category: Ribosome biogenesis]]
		+	[[Category: Rrna processing]]
		+	[[Category: Scnep1]]
		+	[[Category: Spout]]

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

OCA — Wed, 13 Apr 2011 04:39:36 GMT

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

←Older revision

Revision as of 04:39, 13 April 2011

OCA at 04:39, 13 April 2011

OCA — Wed, 13 Apr 2011 04:39:35 GMT

←Older revision		Revision as of 04:39, 13 April 2011
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-	~~{{Seed}}~~	+	[[Image:3oin.png\|left\|200px]]
-	[[Image:3oin.~~jpg~~\|left\|200px]]	+

	<!--		<!--
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	===Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA===		===Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21087996}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21087996 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21087996}}

	==About this Structure==		==About this Structure==
-	~~3OIN~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA].	+	[[3oin]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21087996</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: LaRonde-LeBlanc, N.]]		[[Category: LaRonde-LeBlanc, N.]]
	[[Category: Thomas, S R.]]		[[Category: Thomas, S R.]]
-	[[Category: Emg1]]
-	[[Category: Methyltransferase]]
-	[[Category: Ribosomal protein]]
-	[[Category: Ribosome biogenesis]]
-	[[Category: Rrna processing]]
-	[[Category: Scnep1]]
-	[[Category: Spout]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 1 11:34:12 2010''

OCA at 08:22, 1 December 2010

OCA — Wed, 01 Dec 2010 08:22:26 GMT

←Older revision		Revision as of 08:22, 1 December 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3oin.jpg\|left\|200px]]

-	The ~~entry 3oin~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3oin", 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_3oin\| PDB=3oin \| SCENE= }}

-	~~Authors: Thomas,~~ S~~.R., LaRonde~~-~~LeBlanc, N.~~	+	===Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA===

-	Description: Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Nov 24 13~~:55:42 2010''	+	==About this Structure==
		+	3OIN is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA].
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: LaRonde-LeBlanc, N.]]
		+	[[Category: Thomas, S R.]]
		+	[[Category: Emg1]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Ribosomal protein]]
		+	[[Category: Ribosome biogenesis]]
		+	[[Category: Rrna processing]]
		+	[[Category: Scnep1]]
		+	[[Category: Spout]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 1 11:34:12 2010''

←Older revision		Revision as of 10:44, 18 May 2022
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	<StructureSection load='3oin' size='340' side='right'caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3oin' size='340' side='right'caption='[[3oin]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3OIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3oin]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OIN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3o7b\|3o7b]], [[3oii\|3oii]], [[3oij\|3oij]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">EMG1, NEP1, YLR186W, L9470.5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/rRNA_small_subunit_pseudouridine_methyltransferase_Nep1 rRNA small subunit pseudouridine methyltransferase Nep1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.260 2.1.1.260] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [~~http~~://pdbe.org/3oin PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3oin PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3oin 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=3oin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oin OCA], [https://pdbe.org/3oin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oin RCSB], [https://www.ebi.ac.uk/pdbsum/3oin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oin ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref>	+	[[https://www.uniprot.org/uniprot/NEP1_YEAST NEP1_YEAST]] S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.<ref>PMID:11694595</ref> <ref>PMID:11935223</ref> <ref>PMID:15590835</ref> <ref>PMID:20972225</ref> <ref>PMID:21087996</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==