2pko - Revision history

OCA at 11:03, 30 August 2023

OCA — Wed, 30 Aug 2023 11:03:41 GMT

←Older revision		Revision as of 11:03, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2pko' size='340' side='right'caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2pko' size='340' side='right'caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKO FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~URM1 (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=4932 ATCC 18824])~~</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]] 1.8Å</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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [https://pdbe.org/2pko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [https://www.ebi.ac.uk/pdbsum/2pko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pko 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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [https://pdbe.org/2pko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [https://www.ebi.ac.uk/pdbsum/2pko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/URM1_YEAST URM1_YEAST]] Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions. Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. May also act as an ubiquitin-like protein that is covalently conjugated to other proteins such as AHP1; the relevance of such function is however unclear in vivo. Indirectly involved in oxidative stress response and regulation of budding and haploid invasive growth.<ref>PMID:10713047</ref> <ref>PMID:14555475</ref> <ref>PMID:14551258</ref> <ref>PMID:18664566</ref> <ref>PMID:18755837</ref> <ref>PMID:19145231</ref> <ref>PMID:19151091</ref>	+	[https://www.uniprot.org/uniprot/URM1_YEAST URM1_YEAST] Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions. Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. May also act as an ubiquitin-like protein that is covalently conjugated to other proteins such as AHP1; the relevance of such function is however unclear in vivo. Indirectly involved in oxidative stress response and regulation of budding and haploid invasive growth.<ref>PMID:10713047</ref> <ref>PMID:14555475</ref> <ref>PMID:14551258</ref> <ref>PMID:18664566</ref> <ref>PMID:18755837</ref> <ref>PMID:19145231</ref> <ref>PMID:19151091</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lake, M W~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Lee, E Y~~]]	+	[[Category: Lake MW]]
-	[[Category: ~~Schindelin, H~~]]	+	[[Category: Lee EY]]
-	[[Category: ~~Beta grasp fold ubiquitin-like protein]]~~	+	[[Category: Schindelin H]]
-	~~[[Category: Protein binding~~]]	+

OCA at 15:26, 17 June 2021

OCA — Thu, 17 Jun 2021 15:26:15 GMT

←Older revision		Revision as of 15:26, 17 June 2021
Line 1:		Line 1:

	==Crystal structure of yeast Urm1 at 1.8 A resolution==		==Crystal structure of yeast Urm1 at 1.8 A resolution==
-	<StructureSection load='2pko' size='340' side='right' caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2pko' size='340' side='right'caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKO FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([https://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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [~~http~~://pdbe.org/2pko PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pko PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pko 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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [https://pdbe.org/2pko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [https://www.ebi.ac.uk/pdbsum/2pko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/URM1_YEAST URM1_YEAST]] Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions. Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. May also act as an ubiquitin-like protein that is covalently conjugated to other proteins such as AHP1; the relevance of such function is however unclear in vivo. Indirectly involved in oxidative stress response and regulation of budding and haploid invasive growth.<ref>PMID:10713047</ref> <ref>PMID:14555475</ref> <ref>PMID:14551258</ref> <ref>PMID:18664566</ref> <ref>PMID:18755837</ref> <ref>PMID:19145231</ref> <ref>PMID:19151091</ref>	+	[[https://www.uniprot.org/uniprot/URM1_YEAST URM1_YEAST]] Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions. Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. May also act as an ubiquitin-like protein that is covalently conjugated to other proteins such as AHP1; the relevance of such function is however unclear in vivo. Indirectly involved in oxidative stress response and regulation of budding and haploid invasive growth.<ref>PMID:10713047</ref> <ref>PMID:14555475</ref> <ref>PMID:14551258</ref> <ref>PMID:18664566</ref> <ref>PMID:18755837</ref> <ref>PMID:19145231</ref> <ref>PMID:19151091</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Lake, M W]]		[[Category: Lake, M W]]
	[[Category: Lee, E Y]]		[[Category: Lee, E Y]]

OCA at 08:19, 29 August 2018

OCA — Wed, 29 Aug 2018 08:19:21 GMT

←Older revision		Revision as of 08:19, 29 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of yeast Urm1 at 1.8 A resolution==		==Crystal structure of yeast Urm1 at 1.8 A resolution==
	<StructureSection load='2pko' size='340' side='right' caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2pko' size='340' side='right' caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PKO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PKO FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [http://pdbe.org/2pko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [http://www.ebi.ac.uk/pdbsum/2pko 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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [http://pdbe.org/2pko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [http://www.ebi.ac.uk/pdbsum/2pko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/2pko_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/2pko_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 19:31, 8 February 2016

OCA — Mon, 08 Feb 2016 19:31:36 GMT

←Older revision		Revision as of 19:31, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pko ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:42, 10 September 2015

OCA — Thu, 10 Sep 2015 14:42:46 GMT

←Older revision		Revision as of 14:42, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2pko' size='340' side='right' caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2pko' size='340' side='right' caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PKO FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [http://www.ebi.ac.uk/pdbsum/2pko 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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [http://pdbe.org/2pko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [http://www.ebi.ac.uk/pdbsum/2pko PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 2pko" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Lake, M W]]		[[Category: Lake, M W]]
	[[Category: Lee, E Y]]		[[Category: Lee, E Y]]

OCA at 01:39, 25 December 2014

OCA — Thu, 25 Dec 2014 01:39:41 GMT

←Older revision		Revision as of 01:39, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PKO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PKO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [http://www.ebi.ac.uk/pdbsum/2pko 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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [http://www.ebi.ac.uk/pdbsum/2pko PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/URM1_YEAST URM1_YEAST]] Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions. Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by UBA4. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Prior mcm(5) tRNA modification by the elongator complex is required for 2-thiolation. May also act as an ubiquitin-like protein that is covalently conjugated to other proteins such as AHP1; the relevance of such function is however unclear in vivo. Indirectly involved in oxidative stress response and regulation of budding and haploid invasive growth.<ref>PMID:10713047</ref> <ref>PMID:14555475</ref> <ref>PMID:14551258</ref> <ref>PMID:18664566</ref> <ref>PMID:18755837</ref> <ref>PMID:19145231</ref> <ref>PMID:19151091</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Lake, M W.]]	+	[[Category: Lake, M W]]
-	[[Category: Lee, E Y.]]	+	[[Category: Lee, E Y]]
-	[[Category: Schindelin, H.]]	+	[[Category: Schindelin, H]]
	[[Category: Beta grasp fold ubiquitin-like protein]]		[[Category: Beta grasp fold ubiquitin-like protein]]
	[[Category: Protein binding]]		[[Category: Protein binding]]

OCA at 19:12, 30 September 2014

OCA — Tue, 30 Sep 2014 19:12:58 GMT

←Older revision		Revision as of 19:12, 30 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2pko.~~png\|left~~\|200px]]	+	==Crystal structure of yeast Urm1 at 1.8 A resolution==
		+	<StructureSection load='2pko' size='340' side='right' caption='[[2pko]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pko]] is a 1 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=2PKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PKO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">URM1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2pko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pko RCSB], [http://www.ebi.ac.uk/pdbsum/2pko 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/pk/2pko_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 ==
		+	Because of mechanistic parallels in the activation of ubiquitin and the biosynthesis of several sulfur-containing cofactors, we have characterized the human Urm1 and Saccharomyces cerevisiae Uba4 proteins, which are very similar in sequence to MOCS2A and MOCS3, respectively, two proteins essential for the biosynthesis of the molybdenum cofactor (Moco) in humans. Phylogenetic analyses of MOCS3 homologues showed that Uba4 is the MOCS3 homologue in yeast and thus the only remaining protein of the Moco biosynthetic pathway in this organism. Because of the high levels of sequence identity of human MOCS3 and yeast Uba4, we purified Uba4 and characterized the catalytic activity of the protein in detail. We demonstrate that the C-terminal domain of Uba4, like MOCS3, has rhodanese activity and is able to transfer the sulfur from thiosulfate to cyanide in vitro. In addition, we were able to copurify stable heterotetrameric complexes of Uba4 with both human Urm1 and MOCS2A. The N-terminal domain of Uba4 catalyzes the activation of either MOCS2A or Urm1 by formation of an acyl-adenylate bond. After adenylation, persulfurated Uba4 was able to form a thiocarboxylate group at the C-terminal glycine of either Urm1 or MOCS2A. The formation of a thioester intermediate between Uba4 and Urm1 or MOCS2A was not observed. The functional similarities between Uba4 and MOCS3 further demonstrate the evolutionary link between ATP-dependent protein conjugation and ATP-dependent cofactor sulfuration.

-	~~{{STRUCTURE_2pko\| PDB=2pko \| SCENE= }}~~	+	The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins.,Schmitz J, Chowdhury MM, Hanzelmann P, Nimtz M, Lee EY, Schindelin H, Leimkuhler S Biochemistry. 2008 Jun 17;47(24):6479-89. Epub 2008 May 21. PMID:18491921<ref>PMID:18491921</ref>

-	~~===Crystal structure~~ of ~~yeast Urm1 at 1~~.~~8 A resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18491921}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2pko]] is a 1 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=2PKO OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018491921<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Lake, M W.]]		[[Category: Lake, M W.]]

OCA: Protected "2pko" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 14:09:39 GMT

Protected "2pko" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:09, 7 January 2013

OCA at 14:09, 7 January 2013

OCA — Mon, 07 Jan 2013 14:09:37 GMT

←Older revision		Revision as of 14:09, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2pko.png\|left\|200px]]		[[Image:2pko.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2pko", 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_2pko\| PDB=2pko \| SCENE= }}		{{STRUCTURE_2pko\| PDB=2pko \| SCENE= }}

	===Crystal structure of yeast Urm1 at 1.8 A resolution===		===Crystal structure of yeast Urm1 at 1.8 A resolution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18491921}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18491921 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18491921}}		{{ABSTRACT_PUBMED_18491921}}

	==About this Structure==		==About this Structure==
-	~~2PKO~~ is a 1 chain structure of 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=2PKO OCA].	+	[[2pko]] is a 1 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=2PKO OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18491921~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018491921</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Lake, M W.]]		[[Category: Lake, M W.]]
Line 30:		Line 18:
	[[Category: Beta grasp fold ubiquitin-like protein]]		[[Category: Beta grasp fold ubiquitin-like protein]]
	[[Category: Protein binding]]		[[Category: Protein binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:24:08 2009''

OCA at 00:24, 17 February 2009

OCA — Tue, 17 Feb 2009 00:24:10 GMT

←Older revision		Revision as of 00:24, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2PKO is a ~~[[Single protein]]~~ structure of 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=2PKO OCA].	+	2PKO is a 1 chain structure of 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=2PKO OCA].

	==Reference==		==Reference==
-	The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins., Schmitz J, Chowdhury MM, Hanzelmann P, Nimtz M, Lee EY, Schindelin H, Leimkuhler S, Biochemistry. 2008 Jun 17;47(24):6479-89. Epub 2008 May 21. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18491921 18491921]~~	+	<ref group="xtra">PMID:18491921</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Single protein]]
	[[Category: Lake, M W.]]		[[Category: Lake, M W.]]
	[[Category: Lee, E Y.]]		[[Category: Lee, E Y.]]
Line 32:		Line 31:
	[[Category: Protein binding]]		[[Category: Protein binding]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2 21~~:23:~~36 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 02:24:08 2009''