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| | ==Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with AMP at 1.801 Angstroem resolution== | | ==Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with AMP at 1.801 Angstroem resolution== |
| - | <StructureSection load='4d7a' size='340' side='right' caption='[[4d7a]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='4d7a' size='340' side='right'caption='[[4d7a]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4d7a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D7A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D7A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4d7a]] 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=4D7A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D7A 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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.801Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d79|4d79]]</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4d7a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7a OCA], [http://pdbe.org/4d7a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d7a RCSB], [http://www.ebi.ac.uk/pdbsum/4d7a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7a 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=4d7a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d7a OCA], [https://pdbe.org/4d7a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d7a RCSB], [https://www.ebi.ac.uk/pdbsum/4d7a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d7a 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: Arda, A]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Bruix, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Coll, M]] | + | [[Category: Arda A]] |
| - | [[Category: Fernandez, F J]] | + | [[Category: Bruix M]] |
| - | [[Category: Jimenez-Barbero, J]] | + | [[Category: Coll M]] |
| - | [[Category: Lopez-Estepa, M]] | + | [[Category: Fernandez FJ]] |
| - | [[Category: Round, A]] | + | [[Category: Jimenez-Barbero J]] |
| - | [[Category: Savko, M]] | + | [[Category: Lopez-Estepa M]] |
| - | [[Category: Shepard, W]] | + | [[Category: Round A]] |
| - | [[Category: Vega, M C]] | + | [[Category: Savko M]] |
| - | [[Category: L-cysteine desulfurase]]
| + | [[Category: Shepard W]] |
| - | [[Category: Ligase]]
| + | [[Category: Vega MC]] |
| - | [[Category: Sulfur trafficking]]
| + | |
| - | [[Category: Transpersulfuration]]
| + | |
| Structural highlights
4d7a is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.801Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
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
Cyclic N6-threonylcarbamoyladenosine ('cyclic t6A', ct6A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct6A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct6A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t6A to form ct6A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K+ and Na+ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t6A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct6A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.
The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily.,Lopez-Estepa M, Arda A, Savko M, Round A, Shepard WE, Bruix M, Coll M, Fernandez FJ, Jimenez-Barbero J, Vega MC PLoS One. 2015 Apr 21;10(4):e0118606. doi: 10.1371/journal.pone.0118606., eCollection 2015. PMID:25897750[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
- ↑ Lopez-Estepa M, Arda A, Savko M, Round A, Shepard WE, Bruix M, Coll M, Fernandez FJ, Jimenez-Barbero J, Vega MC. The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily. PLoS One. 2015 Apr 21;10(4):e0118606. doi: 10.1371/journal.pone.0118606., eCollection 2015. PMID:25897750 doi:http://dx.doi.org/10.1371/journal.pone.0118606
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