6n9a
From Proteopedia
(Difference between revisions)
| (One intermediate revision not shown.) | |||
| Line 3: | Line 3: | ||
<StructureSection load='6n9a' size='340' side='right'caption='[[6n9a]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='6n9a' size='340' side='right'caption='[[6n9a]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6n9a]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9A OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[6n9a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N9A FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AE3:2-(2-ETHOXYETHOXY)ETHANOL'>AE3</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=KG4:5-O-[(R)-(carboxyoxy)(hydroxy)phosphoryl]adenosine'>KG4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AE3:2-(2-ETHOXYETHOXY)ETHANOL'>AE3</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=KG4:5-O-[(R)-(carboxyoxy)(hydroxy)phosphoryl]adenosine'>KG4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6n9a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9a OCA], [https://pdbe.org/6n9a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n9a RCSB], [https://www.ebi.ac.uk/pdbsum/6n9a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9a ProSAT]</span></td></tr> |
</table> | </table> | ||
== Function == | == Function == | ||
| - | [ | + | [https://www.uniprot.org/uniprot/TSAB_THEMA TSAB_THEMA] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE; this reaction does not require ATP in vitro. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD (By similarity). |
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The universally conserved N6-threonylcarbamoyladenosine (t6A) modification of tRNA is essential for translational fidelity. In bacteria, t6A biosynthesis starts with the TsaC/TsaC2-catalyzed synthesis of the intermediate threonylcarbamoyl adenylate (TC-AMP), followed by transfer of the threonylcarbamoyl (TC) moiety to adenine-37 of tRNA by the TC-transfer complex comprised of TsaB, TsaD and TsaE subunits and possessing an ATPase activity required for multi-turnover of the t6A cycle. We report a 2.5-A crystal structure of the T. maritima TC-transfer complex (TmTsaB2D2E2) bound to Mg2+-ATP in the ATPase site, and substrate analog carboxy-AMP in the TC-transfer site. Site directed mutagenesis results show that residues in the conserved Switch I and Switch II motifs of TsaE mediate the ATP hydrolysis-driven reactivation/reset step of the t6A cycle. Further, SAXS analysis of the TmTsaB2D2-tRNA complex in solution reveals bound tRNA lodged in the TsaE binding cavity, confirming our previous biochemical data. Based on the crystal structure and molecular docking of TC-AMP and adenine-37 in the TC-transfer site, we propose a model for the mechanism of TC transfer by this universal biosynthetic system. | ||
| + | |||
| + | Conformational communication mediates the reset step in t6A biosynthesis.,Luthra A, Paranagama N, Swinehart W, Bayooz S, Phan P, Quach V, Schiffer JM, Stec B, Iwata-Reuyl D, Swairjo MA Nucleic Acids Res. 2019 May 22. pii: 5494771. doi: 10.1093/nar/gkz439. PMID:31114923<ref>PMID:31114923</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6n9a" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Thermotoga maritima]] |
| - | [[Category: | + | [[Category: Stec B]] |
| - | [[Category: | + | [[Category: Swairjo MA]] |
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Crystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TsaB2D2E2 bound to ATP and carboxy-AMP
| |||||||||||
