2d1p - Revision history

OCA at 13:45, 13 March 2024

2024-03-13T13:45:42Z

←Older revision		Revision as of 13:45, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2d1p' size='340' side='right'caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='2d1p' size='340' side='right'caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.15Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yheN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895]), yheM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=562 "Bacillus coli" Migula 1895]), yheL ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [https://pdbe.org/2d1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [https://www.ebi.ac.uk/pdbsum/2d1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1p 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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [https://pdbe.org/2d1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [https://www.ebi.ac.uk/pdbsum/2d1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TUSD_ECOLI TUSD_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE.<ref>PMID:16387657</ref> [[https://www.uniprot.org/uniprot/TUSB_ECOLI TUSB_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref> [[https://www.uniprot.org/uniprot/TUSC_ECOLI TUSC_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref>	+	[https://www.uniprot.org/uniprot/TUSD_ECOLI TUSD_ECOLI] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE.<ref>PMID:16387657</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d1p 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=2d1p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2-thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl-tRNA synthetases. Recent Escherichia coli genetic studies revealed that the products of five novel genes, tusABCDE, function in the s2U modification. Here, we solved the 2.15 angstroms crystal structure of the E. coli TusBCD complex, a sulfur transfer mediator, forming a heterohexamer composed of a dimer of the heterotrimer. Structure-based sequence alignment suggested two putative active site Cys residues, Cys79 (in TusC) and Cys78 (in TusD), which are exposed on the hexameric complex. In vivo mutant analyses revealed that only Cys78, in the TusD subunit, participates in sulfur transfer during the s2U modification process. Since the single Cys acts as a catalytic residue, we proposed that TusBCD mediates sulfur relay via a putative persulfide state of the TusD subunit.
-
-	Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex.,Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O Structure. 2006 Feb;14(2):357-66. PMID:16472754<ref>PMID:16472754</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2d1p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fukai, S]]	+	[[Category: Fukai S]]
-	[[Category: Ikeuchi, Y]]	+	[[Category: Ikeuchi Y]]
-	[[Category: Numata, T]]	+	[[Category: Numata T]]
-	[[Category: Nureki, O]]	+	[[Category: Nureki O]]
-	[[Category: Suzuki, T]]	+	[[Category: Suzuki T]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Sulfur transfer]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Trna modification~~]]	+

OCA at 11:53, 3 February 2021

2021-02-03T11:53:21Z

←Older revision		Revision as of 11:53, 3 February 2021
Line 1:		Line 1:

	==crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification==		==crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification==
-	<StructureSection load='2d1p' size='340' side='right' caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='2d1p' size='340' side='right'caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2D1P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheM ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheL ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [~~http~~://pdbe.org/2d1p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d1p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1p 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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [https://pdbe.org/2d1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [https://www.ebi.ac.uk/pdbsum/2d1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TUSD_ECOLI TUSD_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE.<ref>PMID:16387657</ref> [[~~http~~://www.uniprot.org/uniprot/TUSB_ECOLI TUSB_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref> [[~~http~~://www.uniprot.org/uniprot/TUSC_ECOLI TUSC_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref>	+	[[https://www.uniprot.org/uniprot/TUSD_ECOLI TUSD_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE.<ref>PMID:16387657</ref> [[https://www.uniprot.org/uniprot/TUSB_ECOLI TUSB_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref> [[https://www.uniprot.org/uniprot/TUSC_ECOLI TUSC_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Ikeuchi, Y]]		[[Category: Ikeuchi, Y]]

OCA at 06:18, 30 May 2018

2018-05-30T06:18:10Z

←Older revision		Revision as of 06:18, 30 May 2018
Line 1:		Line 1:
		+
	==crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification==		==crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification==
	<StructureSection load='2d1p' size='340' side='right' caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='2d1p' size='340' side='right' caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://pdbe.org/2d1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p 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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://pdbe.org/2d1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/2d1p_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d1/2d1p_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>
	</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=2d1p ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:43, 11 September 2015

2015-09-11T23:43:53Z

←Older revision		Revision as of 23:43, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2d1p' size='340' side='right' caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='2d1p' size='340' side='right' caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p 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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://pdbe.org/2d1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TUSD_ECOLI TUSD_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE.<ref>PMID:16387657</ref> [[http://www.uniprot.org/uniprot/TUSB_ECOLI TUSB_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref> [[http://www.uniprot.org/uniprot/TUSC_ECOLI TUSC_ECOLI]] Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions.<ref>PMID:16387657</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 27:
	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 2d1p" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Fukai, S]]		[[Category: Fukai, S]]
	[[Category: Ikeuchi, Y]]		[[Category: Ikeuchi, Y]]

OCA at 16:18, 15 January 2015

2015-01-15T16:18:52Z

←Older revision		Revision as of 16:18, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1P FirstGlance]. <br>		<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1P FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p 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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Fukai, S.]]	+	[[Category: Fukai, S]]
-	[[Category: Ikeuchi, Y.]]	+	[[Category: Ikeuchi, Y]]
-	[[Category: Numata, T.]]	+	[[Category: Numata, T]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: Suzuki, T.]]	+	[[Category: Suzuki, T]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Sulfur transfer]]		[[Category: Sulfur transfer]]
	[[Category: Translation]]		[[Category: Translation]]
	[[Category: Trna modification]]		[[Category: Trna modification]]

OCA at 23:55, 29 September 2014

2014-09-29T23:55:29Z

←Older revision		Revision as of 23:55, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2d1p.~~png~~\|~~left~~\|200px]]	+	==crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification==
		+	<StructureSection load='2d1p' size='340' side='right' caption='[[2d1p]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2d1p]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D1P FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yheN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), yheL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=2d1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1p OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d1p RCSB], [http://www.ebi.ac.uk/pdbsum/2d1p 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/d1/2d1p_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 ==
		+	Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2-thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl-tRNA synthetases. Recent Escherichia coli genetic studies revealed that the products of five novel genes, tusABCDE, function in the s2U modification. Here, we solved the 2.15 angstroms crystal structure of the E. coli TusBCD complex, a sulfur transfer mediator, forming a heterohexamer composed of a dimer of the heterotrimer. Structure-based sequence alignment suggested two putative active site Cys residues, Cys79 (in TusC) and Cys78 (in TusD), which are exposed on the hexameric complex. In vivo mutant analyses revealed that only Cys78, in the TusD subunit, participates in sulfur transfer during the s2U modification process. Since the single Cys acts as a catalytic residue, we proposed that TusBCD mediates sulfur relay via a putative persulfide state of the TusD subunit.

-	~~{{STRUCTURE_2d1p\| PDB=2d1p \| SCENE= }}~~	+	Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex.,Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O Structure. 2006 Feb;14(2):357-66. PMID:16472754<ref>PMID:16472754</ref>

-	~~===crystal structure~~ of ~~heterohexameric TusBCD proteins, which are crucial for~~ the ~~tRNA modification===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16472754}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2d1p]] is a 9 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016472754<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Fukai, S.]]		[[Category: Fukai, S.]]

OCA: Protected "2d1p" [edit=sysop:move=sysop]

2013-01-06T09:24:02Z

Protected "2d1p" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:24, 6 January 2013

OCA at 09:23, 6 January 2013

2013-01-06T09:23:59Z

←Older revision		Revision as of 09:23, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2d1p.png\|left\|200px]]		[[Image:2d1p.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2d1p", 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_2d1p\| PDB=2d1p \| SCENE= }}		{{STRUCTURE_2d1p\| PDB=2d1p \| SCENE= }}

	===crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification===		===crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16472754}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16472754 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16472754}}		{{ABSTRACT_PUBMED_16472754}}

	==About this Structure==		==About this Structure==
-	~~2D1P~~ is a 9 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA].	+	[[2d1p]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16472754~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016472754</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Fukai, S.]]		[[Category: Fukai, S.]]
Line 32:		Line 20:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Sulfur transfer]]		[[Category: Sulfur transfer]]
		+	[[Category: Translation]]
	[[Category: Trna modification]]		[[Category: Trna modification]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:02:09 2009''

OCA at 05:02, 18 February 2009

2009-02-18T05:02:12Z

←Older revision		Revision as of 05:02, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2D1P is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA].	+	2D1P is a 9 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1P OCA].

	==Reference==		==Reference==
-	~~Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex., Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O, Structure. 2006 Feb;14(2):357-66.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16472754 16472754]~~	+	<ref group="xtra">PMID:16472754</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Protein complex]]
	[[Category: Fukai, S.]]		[[Category: Fukai, S.]]
	[[Category: Ikeuchi, Y.]]		[[Category: Ikeuchi, Y.]]
Line 35:		Line 34:
	[[Category: Trna modification]]		[[Category: Trna modification]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 13~~:49:~~34 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:02:09 2009''

OCA at 10:49, 29 July 2008

2008-07-29T10:49:39Z

←Older revision		Revision as of 10:49, 29 July 2008
Line 1:		Line 1:
-	[[Image:2d1p.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2d1p.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2d1p\| PDB=2d1p \| SCENE= }}		{{STRUCTURE_2d1p\| PDB=2d1p \| SCENE= }}

-	~~'''~~crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification~~'''~~	+	===crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification===


-	~~==Overview==~~	+	<!--
-	~~Uridine at wobble position 34 of tRNA(Lys), tRNA(Glu), and tRNA(Gln) is exclusively modified into 2~~-~~thiouridine (s2U), which is crucial for both precise codon recognition and recognition by the cognate aminoacyl~~-~~tRNA synthetases. Recent Escherichia coli genetic studies revealed that the products of five novel genes~~, ~~tusABCDE~~, ~~function in~~ the ~~s2U modification. Here, we solved~~ the 2.15 angstroms crystal structure of the E. coli TusBCD complex, a sulfur transfer mediator, forming a heterohexamer composed of a dimer of the heterotrimer. Structure-based sequence alignment suggested two putative active site Cys residues, Cys79 (~~in TusC) and Cys78 (in TusD), which are exposed~~ on ~~the hexameric complex~~. ~~In vivo mutant analyses revealed that only Cys78, in the TusD subunit, participates in sulfur transfer during the s2U modification process~~. ~~Since the single Cys acts as a catalytic residue~~, ~~we proposed that TusBCD mediates sulfur relay via a putative persulfide state of~~ the ~~TusD subunit~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_16472754}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 16472754 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_16472754}}

	==About this Structure==		==About this Structure==
Line 30:		Line 34:
	[[Category: Sulfur transfer]]		[[Category: Sulfur transfer]]
	[[Category: Trna modification]]		[[Category: Trna modification]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 23~~:31:46 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:49:34 2008''