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==Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)==
==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=''>
<StructureSection load='6agg' size='340' side='right'caption='[[6agg]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6agg]] 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=6AGG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AGG FirstGlance]. <br>
<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='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=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=ZN:ZINC+ION'>ZN</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]] 2.706&#8491;</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=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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xob|5xob]]</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>
<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='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=6agg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6agg OCA], [http://pdbe.org/6agg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6agg RCSB], [http://www.ebi.ac.uk/pdbsum/6agg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6agg 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: Dong, J S]]
[[Category: Large Structures]]
[[Category: Gong, W M]]
[[Category: Dong JS]]
[[Category: Conformational change]]
[[Category: Gong WM]]
[[Category: Ligase]]
[[Category: Tia]]
[[Category: Trna modification]]
[[Category: Zinc finger engineering]]
[[Category: Zinc ribbon]]

Latest revision as of 12:41, 23 October 2024

Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)

Structural highlights

6agg 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 2.706Å
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

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.

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[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ 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
  2. ↑ 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. Structure of tRNA Modifying Enzyme TiaS and Motions of its Substrate Binding Zinc Ribbon. J Mol Biol. 2018 Aug 16. pii: S0022-2836(18)30961-6. doi:, 10.1016/j.jmb.2018.08.015. PMID:30121296 doi:http://dx.doi.org/10.1016/j.jmb.2018.08.015

6agg, resolution 2.71Å

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