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| | <StructureSection load='3au7' size='340' side='right'caption='[[3au7]], [[Resolution|resolution]] 2.60Å' scene=''> | | <StructureSection load='3au7' size='340' side='right'caption='[[3au7]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3au7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AU7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AU7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3au7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AU7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AU7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</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]] 2.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3amt|3amt]], [[3amu|3amu]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AF_2259 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=3au7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3au7 OCA], [https://pdbe.org/3au7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3au7 RCSB], [https://www.ebi.ac.uk/pdbsum/3au7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3au7 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=3au7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3au7 OCA], [https://pdbe.org/3au7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3au7 RCSB], [https://www.ebi.ac.uk/pdbsum/3au7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3au7 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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>
| + | [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: Arcfl]] | + | [[Category: Archaeoglobus fulgidus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Numata, T]] | + | [[Category: Numata T]] |
| - | [[Category: Osawa, T]] | + | [[Category: Osawa T]] |
| - | [[Category: Atp hydrolysis]]
| + | |
| - | [[Category: Rna binding protein]]
| + | |
| Structural highlights
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
The cytidine at the first position of the anticodon (C34) in the AUA codon-specific archaeal tRNA(Ile2) is modified to 2-agmatinylcytidine (agm(2)C or agmatidine), an agmatine-conjugated cytidine derivative, which is crucial for the precise decoding of the genetic code. Agm(2)C is synthesized by tRNA(Ile)-agm(2)C synthetase (TiaS) in an ATP-dependent manner. Here we present the crystal structures of the Archaeoglobus fulgidus TiaS-tRNA(Ile2) complexed with ATP, or with AMPCPP and agmatine, revealing a previously unknown kinase module required for activating C34 by phosphorylation, and showing the molecular mechanism by which TiaS discriminates between tRNA(Ile2) and tRNA(Met). In the TiaS-tRNA(Ile2)-ATP complex, C34 is trapped within a pocket far away from the ATP-binding site. In the agmatine-containing crystals, C34 is located near the AMPCPP gamma-phosphate in the kinase module, demonstrating that agmatine is essential for placing C34 in the active site. These observations also provide the structural dynamics for agm(2)C formation.
Structural basis of tRNA agmatinylation essential for AUA codon decoding.,Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T Nat Struct Mol Biol. 2011 Oct 16;18(11):1275-80. doi: 10.1038/nsmb.2144. PMID:22002223[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
- ↑ Osawa T, Kimura S, Terasaka N, Inanaga H, Suzuki T, Numata T. Structural basis of tRNA agmatinylation essential for AUA codon decoding. Nat Struct Mol Biol. 2011 Oct 16;18(11):1275-80. doi: 10.1038/nsmb.2144. PMID:22002223 doi:10.1038/nsmb.2144
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