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'''Unreleased structure'''


The entry 5xob is ON HOLD until Aug 29 2019
==Crystal structure of apo TiaS (tRNAIle2 agmatidine synthetase)==
<StructureSection load='5xob' size='340' side='right' caption='[[5xob]], [[Resolution|resolution]] 2.48&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5xob]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XOB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XOB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6agg|6agg]]</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=5xob FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xob OCA], [http://pdbe.org/5xob PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xob RCSB], [http://www.ebi.ac.uk/pdbsum/5xob PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xob ProSAT]</span></td></tr>
</table>
== 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>  
<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.
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 apo TiaS (tRNAIle2 agmatidine synthetase)
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5xob" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Dong, J]]
[[Category: Dong, J]]
[[Category: Conformational change]]
[[Category: Ligase]]
[[Category: Tia]]
[[Category: Trna modification]]
[[Category: Zinc finger engineering]]
[[Category: Zinc ribbon]]

Revision as of 10:17, 29 August 2018

Crystal structure of apo TiaS (tRNAIle2 agmatidine synthetase)Crystal structure of apo TiaS (tRNAIle2 agmatidine synthetase)

Structural highlights

5xob is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:
Activity:tRNA(Ile)(2)-agmatinylcytidine synthase, with EC number 6.3.4.22
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

5xob, resolution 2.48Å

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