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| | <StructureSection load='4yed' size='340' side='right'caption='[[4yed]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='4yed' size='340' side='right'caption='[[4yed]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4yed]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YED FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4yed]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YED FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yed OCA], [https://pdbe.org/4yed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yed RCSB], [https://www.ebi.ac.uk/pdbsum/4yed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yed ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rdi|4rdi]], [[4rdh|4rdh]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tcdA, csdL, ygdL, b2812, JW2783 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yed OCA], [http://pdbe.org/4yed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yed RCSB], [http://www.ebi.ac.uk/pdbsum/4yed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yed ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TCDA_ECOLI TCDA_ECOLI]] Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine. TcdA is also part of a sulfur transfer pathway; is able to accept sulfur from CsdA directly in vitro, but CsdE might act as the sulfur donor in vivo.<ref>PMID:20054882</ref> <ref>PMID:23242255</ref> | + | [https://www.uniprot.org/uniprot/TCDA_ECOLI TCDA_ECOLI] Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine. TcdA is also part of a sulfur transfer pathway; is able to accept sulfur from CsdA directly in vitro, but CsdE might act as the sulfur donor in vivo.<ref>PMID:20054882</ref> <ref>PMID:23242255</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: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kim, S]] | + | [[Category: Kim S]] |
| - | [[Category: Park, S Y]] | + | [[Category: Park SY]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: N6-threonylcarbamoyladenosine dehydratase trna modification]]
| + | |
| Structural highlights
Function
TCDA_ECOLI Catalyzes the ATP-dependent dehydration of threonylcarbamoyladenosine at position 37 (t(6)A37) to form cyclic t(6)A37 (ct(6)A37) in tRNAs that read codons beginning with adenine. TcdA is also part of a sulfur transfer pathway; is able to accept sulfur from CsdA directly in vitro, but CsdE might act as the sulfur donor in vivo.[1] [2]
Publication Abstract from PubMed
Escherichia coli TcdA (also known as CsdL) was previously shown to catalyze the ATP-dependent dehydration/cyclization of hypermodified tRNA N6-threonylcarbamoyladenosine into further cyclic N6-threonylcarbamoyladenosine. In this study, we report the X-ray crystal structures of E. coli TcdA with either AMP or ATP bound. The AMP/ATP-bound N-terminal sub-domain of TcdA resembles the ATP-binding Rossmann fold of E. coli ThiF and MoeB that are enzymes respectively taking part in the biosynthesis of thiamine and molybdopterin; however, the remaining C-terminal sub-domain of TcdA adopts a structure unrelated to any other known folds. In TcdA, the ATP-utilizing adenylation of tRNA N6-threonylcarbamoyladenosine and a subsequent thioester formation via an active cysteine, similar to the mechanisms in ThiF and MoeB, could take place for the dehydratase function. Analysis of the structure with sequence alignment suggests the disordered Cys234 of TcdA as the most likely catalytic residue. The structure further indicates that the C-terminal sub-domain can provide a binding interface for the tRNA substrate. Binding study using the surface mutants of TcdA and tRNA reveals that the positively charged regions of mainly the C-terminal sub-domain are important for the tRNA recognition.
The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N-Threonylcarbamoyladenosine Dehydratase Activity.,Kim S, Lee H, Park S J Mol Biol. 2015 Jun 21. pii: S0022-2836(15)00345-9. doi:, 10.1016/j.jmb.2015.06.005. PMID:26101842[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Trotter V, Vinella D, Loiseau L, Ollagnier de Choudens S, Fontecave M, Barras F. The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein. Mol Microbiol. 2009 Dec;74(6):1527-42. PMID:20054882
- ↑ Miyauchi K, Kimura S, Suzuki T. A cyclic form of N6-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol. 2013 Feb;9(2):105-11. doi: 10.1038/nchembio.1137. Epub 2012 Dec, 16. PMID:23242255 doi:http://dx.doi.org/10.1038/nchembio.1137
- ↑ Kim S, Lee H, Park S. The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N-Threonylcarbamoyladenosine Dehydratase Activity. J Mol Biol. 2015 Jun 21. pii: S0022-2836(15)00345-9. doi:, 10.1016/j.jmb.2015.06.005. PMID:26101842 doi:http://dx.doi.org/10.1016/j.jmb.2015.06.005
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