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| | <StructureSection load='4rvz' size='340' side='right'caption='[[4rvz]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='4rvz' size='340' side='right'caption='[[4rvz]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4rvz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RVZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RVZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4rvz]] 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=4RVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RVZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ZNN:N-(4-AMINOBUTYL)-2-AZIDOACETAMIDE'>ZNN</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]] 2.9Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=ZNN:N-(4-AMINOBUTYL)-2-AZIDOACETAMIDE'>ZNN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tiaS, AF_2259 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</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=4rvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rvz OCA], [https://pdbe.org/4rvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rvz RCSB], [https://www.ebi.ac.uk/pdbsum/4rvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rvz ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA(Ile)(2)-agmatinylcytidine_synthase tRNA(Ile)(2)-agmatinylcytidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.22 6.3.4.22] </span></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=4rvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rvz OCA], [http://pdbe.org/4rvz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rvz RCSB], [http://www.ebi.ac.uk/pdbsum/4rvz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rvz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arcfu]] | + | [[Category: Archaeoglobus fulgidus DSM 4304]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Dong, J]] | + | [[Category: Dong J]] |
| - | [[Category: Gong, W]] | + | [[Category: Gong W]] |
| - | [[Category: Li, F]] | + | [[Category: Li F]] |
| - | [[Category: Wang, J]] | + | [[Category: Wang J]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Phosphorylation]]
| + | |
| - | [[Category: Tia]]
| + | |
| - | [[Category: Trna modification]]
| + | |
| Structural highlights
4rvz is a 1 chain structure with sequence from Archaeoglobus fulgidus DSM 4304. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.9Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[1]
Publication Abstract from PubMed
Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported for the site- and sequence-specific covalent labeling of RNAs in mammalian cells by using tRNAIle2 -agmatidine synthetase (Tias) and click chemistry. The crystal structure of Tias in complex with an azide-bearing agmatine analogue was solved to unravel the structural basis for Tias/substrate recognition. The unique RNA sequence specificity and plastic Tias/substrate recognition enable the site-specific transfer of azide/alkyne groups to an RNA molecule of interest in vitro and in mammalian cells. Subsequent click chemistry reactions facilitate the versatile labeling, functionalization, and visualization of target RNA.
A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells.,Li F, Dong J, Hu X, Gong W, Li J, Shen J, Tian H, Wang J Angew Chem Int Ed Engl. 2015 Feb 18. doi: 10.1002/anie.201410433. PMID:25694369[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T. Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat Chem Biol. 2010 Apr;6(4):277-82. doi: 10.1038/nchembio.323. Epub 2010 Feb 7. PMID:20139989 doi:10.1038/nchembio.323
- ↑ Li F, Dong J, Hu X, Gong W, Li J, Shen J, Tian H, Wang J. A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells. Angew Chem Int Ed Engl. 2015 Feb 18. doi: 10.1002/anie.201410433. PMID:25694369 doi:http://dx.doi.org/10.1002/anie.201410433
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