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5b4f: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5b4f]] 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=5B4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4F FirstGlance]. <br>
<table><tr><td colspan='2'>[[5b4f]] 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=5B4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B4F FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.75&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=5b4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4f OCA], [https://pdbe.org/5b4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4f RCSB], [https://www.ebi.ac.uk/pdbsum/5b4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4f 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=5b4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b4f OCA], [https://pdbe.org/5b4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b4f RCSB], [https://www.ebi.ac.uk/pdbsum/5b4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b4f 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>  
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== 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5b4f" style="background-color:#fffaf0;"></div>
== References ==
== References ==
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