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| | ==Crystal structure of ph0300== | | ==Crystal structure of ph0300== |
| - | <StructureSection load='3vrh' size='340' side='right' caption='[[3vrh]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3vrh' size='340' side='right'caption='[[3vrh]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VRH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vrh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VRH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VRH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCN:BICINE'>BCN</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]] 2.1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH0300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCN:BICINE'>BCN</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [http://pdbe.org/3vrh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [http://www.ebi.ac.uk/pdbsum/3vrh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrh 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=3vrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vrh OCA], [https://pdbe.org/3vrh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vrh RCSB], [https://www.ebi.ac.uk/pdbsum/3vrh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vrh ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/TTUA_PYRHO TTUA_PYRHO] 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:28655838). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (By similarity). Can use free sulfide as sulfur source in vitro, which may be also the sulfur source in vivo (PubMed:28655838).[UniProtKB:Q72LF3]<ref>PMID:28655838</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus horikoshii]] | + | [[Category: Large Structures]] |
| - | [[Category: Goto-Ito, S]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Ito, T]] | + | [[Category: Goto-Ito S]] |
| - | [[Category: Kuratani, M]] | + | [[Category: Ito T]] |
| - | [[Category: Nakagawa, H]] | + | [[Category: Kuratani M]] |
| - | [[Category: Sekine, S I]] | + | [[Category: Nakagawa H]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Sekine SI]] |
| - | [[Category: Atpase]]
| + | [[Category: Yokoyama S]] |
| - | [[Category: Rna binding protein]]
| + | |
| - | [[Category: Thiolation]]
| + | |
| - | [[Category: Trna modification enzyme]]
| + | |
| Structural highlights
Function
TTUA_PYRHO 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:28655838). This modification allows thermal stabilization of tRNAs in thermophilic microorganisms, and is required for cell growth at high temperatures (By similarity). Can use free sulfide as sulfur source in vitro, which may be also the sulfur source in vivo (PubMed:28655838).[UniProtKB:Q72LF3][1]
Publication Abstract from PubMed
In thermophilic bacteria, specific 2-thiolation occurs on the conserved ribothymidine at position 54 (T54) in tRNAs, which is necessary for survival at high temperatures. T54 2-thiolation is achieved by the tRNA thiouridine synthetase TtuA and sulfur-carrier proteins. TtuA has five conserved CXXC/H motifs and the signature PP motif, and belongs to the TtcA family of tRNA 2-thiolation enzymes, for which there is currently no structural information. In this study, we determined the crystal structure of a TtuA homologue from the hyperthermophilic archeaon Pyrococcus horikoshii at 2.1 A resolution. The P. horikoshii TtuA forms a homodimer, and each subunit contains a catalytic domain and unique N- and C-terminal zinc fingers. The catalytic domain has much higher structural similarity to that of another tRNA modification enzyme, TilS (tRNA(Ile) (2) lysidine synthetase), than to the other type of tRNA 2-thiolation enzyme, MnmA. Three conserved cysteine residues are clustered in the putative catalytic site, which is not present in TilS. An in vivo mutational analysis in the bacterium Thermus thermophilus demonstrated that the three conserved cysteine residues and the putative ATP-binding residues in the catalytic domain are important for the TtuA activity. A positively-charged surface that includes the catalytic site and the two zinc fingers is likely to provide the tRNA binding site. Proteins 2013. (c) 2013 Wiley Periodicals, Inc.
Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.,Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine SI, Shigi N, Yokoyama S Proteins. 2013 Feb 27. doi: 10.1002/prot.24273. PMID:23444054[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Arragain S, Bimai O, Legrand P, Caillat S, Ravanat JL, Touati N, Binet L, Atta M, Fontecave M, Golinelli-Pimpaneau B. Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster. Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7355-7360. doi:, 10.1073/pnas.1700902114. Epub 2017 Jun 27. PMID:28655838 doi:http://dx.doi.org/10.1073/pnas.1700902114
- ↑ Nakagawa H, Kuratani M, Goto-Ito S, Ito T, Katsura K, Terada T, Shirouzu M, Sekine SI, Shigi N, Yokoyama S. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA. Proteins. 2013 Feb 27. doi: 10.1002/prot.24273. PMID:23444054 doi:http://dx.doi.org/10.1002/prot.24273
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