5b4e - Revision history

OCA at 12:07, 13 August 2026

2026-08-13T12:07:29Z

← Older revision		Revision as of 12:07, 13 August 2026
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4E FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.698Å</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]] 2.698Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA~~</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4~~</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [https://pdbe.org/5b4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [https://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e 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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [https://pdbe.org/5b4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [https://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TTUA_THET2 TTUA_THET2] Catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T) (PubMed:16547008, PubMed:28439027). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (PubMed:16547008). TtuA transfers the S atom from the thiocarboxylated C-terminus of TtuB to tRNA (PubMed:28439027).<ref>PMID:16547008</ref> <ref>PMID:28439027</ref>		[https://www.uniprot.org/uniprot/TTUA_THET2 TTUA_THET2] Catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T) (PubMed:16547008, PubMed:28439027). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (PubMed:16547008). TtuA transfers the S atom from the thiocarboxylated C-terminus of TtuB to tRNA (PubMed:28439027).<ref>PMID:16547008</ref> <ref>PMID:28439027</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Two-thiouridine (s2U) at position 54 of transfer RNA (tRNA) is a posttranscriptional modification that enables thermophilic bacteria to survive in high-temperature environments. s2U is produced by the combined action of two proteins, 2-thiouridine synthetase TtuA and 2-thiouridine synthesis sulfur carrier protein TtuB, which act as a sulfur (S) transfer enzyme and a ubiquitin-like S donor, respectively. Despite the accumulation of biochemical data in vivo, the enzymatic activity by TtuA/TtuB has rarely been observed in vitro, which has hindered examination of the molecular mechanism of S transfer. Here we demonstrate by spectroscopic, biochemical, and crystal structure analyses that TtuA requires oxygen-labile [4Fe-4S]-type iron (Fe)-S clusters for its enzymatic activity, which explains the previously observed inactivation of this enzyme in vitro. The [4Fe-4S] cluster was coordinated by three highly conserved cysteine residues, and one of the Fe atoms was exposed to the active site. Furthermore, the crystal structure of the TtuA-TtuB complex was determined at a resolution of 2.5 A, which clearly shows the S transfer of TtuB to tRNA using its C-terminal thiocarboxylate group. The active site of TtuA is connected to the outside by two channels, one occupied by TtuB and the other used for tRNA binding. Based on these observations, we propose a molecular mechanism of S transfer by TtuA using the ubiquitin-like S donor and the [4Fe-4S] cluster.

			Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA.,Chen M, Asai SI, Narai S, Nambu S, Omura N, Sakaguchi Y, Suzuki T, Ikeda-Saito M, Watanabe K, Yao M, Shigi N, Tanaka Y Proc Natl Acad Sci U S A. 2017 Apr 24. pii: 201615585. doi:, 10.1073/pnas.1615585114. PMID:28439027<ref>PMID:28439027</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5b4e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:07, 20 March 2024

2024-03-20T09:07:21Z

← Older revision		Revision as of 09:07, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.698Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [https://pdbe.org/5b4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [https://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e 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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [https://pdbe.org/5b4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [https://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TTUA_THET2 TTUA_THET2] Catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T) (PubMed:16547008, PubMed:28439027). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (PubMed:16547008). TtuA transfers the S atom from the thiocarboxylated C-terminus of TtuB to tRNA (PubMed:28439027).<ref>PMID:16547008</ref> <ref>PMID:28439027</ref>		[https://www.uniprot.org/uniprot/TTUA_THET2 TTUA_THET2] Catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T) (PubMed:16547008, PubMed:28439027). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (PubMed:16547008). TtuA transfers the S atom from the thiocarboxylated C-terminus of TtuB to tRNA (PubMed:28439027).<ref>PMID:16547008</ref> <ref>PMID:28439027</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Two-thiouridine (s2U) at position 54 of transfer RNA (tRNA) is a posttranscriptional modification that enables thermophilic bacteria to survive in high-temperature environments. s2U is produced by the combined action of two proteins, 2-thiouridine synthetase TtuA and 2-thiouridine synthesis sulfur carrier protein TtuB, which act as a sulfur (S) transfer enzyme and a ubiquitin-like S donor, respectively. Despite the accumulation of biochemical data in vivo, the enzymatic activity by TtuA/TtuB has rarely been observed in vitro, which has hindered examination of the molecular mechanism of S transfer. Here we demonstrate by spectroscopic, biochemical, and crystal structure analyses that TtuA requires oxygen-labile [4Fe-4S]-type iron (Fe)-S clusters for its enzymatic activity, which explains the previously observed inactivation of this enzyme in vitro. The [4Fe-4S] cluster was coordinated by three highly conserved cysteine residues, and one of the Fe atoms was exposed to the active site. Furthermore, the crystal structure of the TtuA-TtuB complex was determined at a resolution of 2.5 A, which clearly shows the S transfer of TtuB to tRNA using its C-terminal thiocarboxylate group. The active site of TtuA is connected to the outside by two channels, one occupied by TtuB and the other used for tRNA binding. Based on these observations, we propose a molecular mechanism of S transfer by TtuA using the ubiquitin-like S donor and the [4Fe-4S] cluster.

	Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA.,Chen M, Asai SI, Narai S, Nambu S, Omura N, Sakaguchi Y, Suzuki T, Ikeda-Saito M, Watanabe K, Yao M, Shigi N, Tanaka Y Proc Natl Acad Sci U S A. 2017 Apr 24. pii: 201615585. doi:, 10.1073/pnas.1615585114. PMID:28439027<ref>PMID:28439027</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5b4e" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:38, 31 May 2023

2023-05-31T06:38:25Z

← Older revision		Revision as of 06:38, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5b4e' size='340' side='right'caption='[[5b4e]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5b4e' size='340' side='right'caption='[[5b4e]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet2 Thet2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b4f\|5b4f]], [[5b4g\|5b4g]]</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [https://pdbe.org/5b4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [https://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</span></td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0106 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])~~</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [~~http~~://pdbe.org/5b4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/TTUA_THET2 TTUA_THET2] Catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T) (PubMed:16547008, PubMed:28439027). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (PubMed:16547008). TtuA transfers the S atom from the thiocarboxylated C-terminus of TtuB to tRNA (PubMed:28439027).<ref>PMID:16547008</ref> <ref>PMID:28439027</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Thet2~~]]		[[Category: Thermus thermophilus HB27]]
	[[Category: Chen, M]]		[[Category: Chen M]]
	[[Category: Narai, S]]		[[Category: Narai S]]
	[[Category: Tanaka, Y]]		[[Category: Tanaka Y]]
	[[Category: Yao, M]]		[[Category: Yao M]]
	~~[[Category: Sulfur transferase]]~~
	~~[[Category: Transferase~~]]

OCA at 08:46, 11 March 2020

2020-03-11T08:46:05Z

← Older revision		Revision as of 08:46, 11 March 2020
Line 1:		Line 1:

	==Sulfur Transferase TtuA in complex with iron sulfur cluster and ATP derivative==		==Sulfur Transferase TtuA in complex with iron sulfur cluster and ATP derivative==
	<StructureSection load='5b4e' size='340' side='right' caption='[[5b4e]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5b4e' size='340' side='right'caption='[[5b4e]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet2 Thet2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B4E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b4f\|5b4f]], [[5b4g\|5b4g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b4f\|5b4f]], [[5b4g\|5b4g]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0106 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=262724 THET2])</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [http://pdbe.org/5b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [http://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [http://pdbe.org/5b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [http://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Thet2]]
	[[Category: Chen, M]]		[[Category: Chen, M]]
	[[Category: Narai, S]]		[[Category: Narai, S]]

OCA at 09:11, 17 May 2017

2017-05-17T09:11:45Z

← Older revision		Revision as of 09:11, 17 May 2017
Line 1:		Line 1:

	==~~Enzyme Veg136 protein~~ in complex with ~~ligand~~==		==Sulfur Transferase TtuA in complex with iron sulfur cluster and ATP derivative==
	<StructureSection load='5b4e' size='340' side='right' caption='[[5b4e]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='5b4e' size='340' side='right' caption='[[5b4e]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [http://pdbe.org/5b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [http://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [http://pdbe.org/5b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [http://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Two-thiouridine (s2U) at position 54 of transfer RNA (tRNA) is a posttranscriptional modification that enables thermophilic bacteria to survive in high-temperature environments. s2U is produced by the combined action of two proteins, 2-thiouridine synthetase TtuA and 2-thiouridine synthesis sulfur carrier protein TtuB, which act as a sulfur (S) transfer enzyme and a ubiquitin-like S donor, respectively. Despite the accumulation of biochemical data in vivo, the enzymatic activity by TtuA/TtuB has rarely been observed in vitro, which has hindered examination of the molecular mechanism of S transfer. Here we demonstrate by spectroscopic, biochemical, and crystal structure analyses that TtuA requires oxygen-labile [4Fe-4S]-type iron (Fe)-S clusters for its enzymatic activity, which explains the previously observed inactivation of this enzyme in vitro. The [4Fe-4S] cluster was coordinated by three highly conserved cysteine residues, and one of the Fe atoms was exposed to the active site. Furthermore, the crystal structure of the TtuA-TtuB complex was determined at a resolution of 2.5 A, which clearly shows the S transfer of TtuB to tRNA using its C-terminal thiocarboxylate group. The active site of TtuA is connected to the outside by two channels, one occupied by TtuB and the other used for tRNA binding. Based on these observations, we propose a molecular mechanism of S transfer by TtuA using the ubiquitin-like S donor and the [4Fe-4S] cluster.

			Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA.,Chen M, Asai SI, Narai S, Nambu S, Omura N, Sakaguchi Y, Suzuki T, Ikeda-Saito M, Watanabe K, Yao M, Shigi N, Tanaka Y Proc Natl Acad Sci U S A. 2017 Apr 24. pii: 201615585. doi:, 10.1073/pnas.1615585114. PMID:28439027<ref>PMID:28439027</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5b4e" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:06, 4 May 2017

2017-05-04T13:06:37Z

← Older revision		Revision as of 13:06, 4 May 2017
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5b4e is ~~ON HOLD until Jun 03 2018~~		==Enzyme Veg136 protein in complex with ligand==
			<StructureSection load='5b4e' size='340' side='right' caption='[[5b4e]], [[Resolution\|resolution]] 2.70Å' scene=''>
	~~Authors~~: ~~Chen~~, M., ~~Narai~~, S., ~~Tanaka~~, Y., ~~Yao, M~~.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5b4e]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B4E FirstGlance]. <br>
	~~Description: Enzyme Veg136 protein in complex with ligand~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~[[Category: Unreleased Structures]]~~		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5b4f\|5b4f]], [[5b4g\|5b4g]]</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=5b4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4e OCA], [http://pdbe.org/5b4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b4e RCSB], [http://www.ebi.ac.uk/pdbsum/5b4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4e ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
	[[Category: Chen, M]]		[[Category: Chen, M]]
			[[Category: Narai, S]]
			[[Category: Tanaka, Y]]
	[[Category: Yao, M]]		[[Category: Yao, M]]
	[[Category: ~~Tanaka, Y~~]]		[[Category: Sulfur transferase]]
	[[Category: ~~Narai, S~~]]		[[Category: Transferase]]

OCA at 07:08, 5 April 2017

2017-04-05T07:08:46Z

← Older revision		Revision as of 07:08, 5 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5b4e is ON HOLD until ~~Paper Publication~~		The entry 5b4e is ON HOLD until Jun 03 2018

	Authors: Chen, M., Narai, S., Tanaka, Y., Yao, M.		Authors: Chen, M., Narai, S., Tanaka, Y., Yao, M.

	Description: ~~ENZYME IN COMPLEX WITH LIGAND~~		Description: Enzyme Veg136 protein in complex with ligand
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Chen, M]]		[[Category: Chen, M]]

OCA at 11:28, 1 February 2017

2017-02-01T11:28:29Z

← Older revision		Revision as of 11:28, 1 February 2017
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	Description: ENZYME IN COMPLEX WITH LIGAND		Description: ENZYME IN COMPLEX WITH LIGAND
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Chen, M]]
	[[Category: Yao, M]]		[[Category: Yao, M]]
			[[Category: Tanaka, Y]]
	[[Category: Narai, S]]		[[Category: Narai, S]]
	~~[[Category: Chen, M]]~~
	~~[[Category: Tanaka, Y]]~~

OCA at 09:33, 1 June 2016

2016-06-01T09:33:31Z

← Older revision		Revision as of 09:33, 1 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5b4e is ON HOLD		The entry 5b4e is ON HOLD until Paper Publication

	Authors: Chen, M., Narai, S., Tanaka, Y., Yao, M.		Authors: Chen, M., Narai, S., Tanaka, Y., Yao, M.

OCA: Protected "5b4e" [edit=sysop:move=sysop]

2016-05-10T20:57:57Z

Protected "5b4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 20:57, 10 May 2016
(No difference)