6agg: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 6agg is ON HOLD
+==Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)==
+<StructureSection load='6agg' size='340' side='right'caption='[[6agg]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6agg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AGG FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.706&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AG2:AGMATINE'>AG2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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=6agg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agg OCA], [https://pdbe.org/6agg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6agg RCSB], [https://www.ebi.ac.uk/pdbsum/6agg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6agg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TIAS_ARCFU TIAS_ARCFU] ATP-dependent agmatine transferase that catalyzes the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2), converting the codon specificity from AUG to AUA.<ref>PMID:20139989</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The accurate modification of the tRNA(Ile) anticodon wobble cytosine 34 is critical for AUA decoding in protein synthesis. Archaeal tRNA(Ile2) cytosine 34 is modified with agmatine in the presence of ATP by TiaS (tRNA(Ile2) agmatidine synthetase). Yet, no structure of apo-form full length TiaS is available currently. Here, the crystal structures of apo TiaS and a complex of TiaS-agmatine-AMPPCP-Mg are presented, with properly folded zinc ribbon and Cys4-zinc coordination identified. Compared with tRNA(Ile2) bound form, the architecture of apo TiaS shows a totally different conformation of zinc ribbon. Molecular dynamics simulations of the docking complex between free-state TiaS and tRNA(Ile2) suggest that zinc ribbon domain is capable of performing large scale motions to sample substrate binding competent conformation. Principle component analysis and normal mode analysis show consistent results about the relative directionality of functionally correlated zinc ribbon motions. Apo TiaS, and TiaS-agmatine-AMPPCP-Mg/TiaS-AMPCPP-Mg complex structures capture two snapshots of the flexible ATP-Mg binding p2loop step by step stabilization. Research from this study provides new insight into TiaS functional mechanism and the dynamic feature of zinc ribbons.
-Authors: Dong, J.S., Gong, W.M.
+Structure of tRNA Modifying Enzyme TiaS and Motions of its Substrate Binding Zinc Ribbon.,Dong J, Li F, Gao F, Wei J, Lin Y, Zhang Y, Lou J, Liu G, Dong Y, Liu L, Liu H, Wang J, Gong W J Mol Biol. 2018 Aug 16. pii: S0022-2836(18)30961-6. doi:, 10.1016/j.jmb.2018.08.015. PMID:30121296<ref>PMID:30121296</ref>
-Description: Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Gong, W.M]]
+<div class="pdbe-citations 6agg" style="background-color:#fffaf0;"></div>
-[[Category: Dong, J.S]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Archaeoglobus fulgidus DSM 4304]]
+[[Category: Large Structures]]
+[[Category: Dong JS]]
+[[Category: Gong WM]]