5XOB

Crystal structure of apo TiaS (tRNAIle2 agmatidine synthetase)

Summary for 5XOB

• Entry DOI: 10.2210/pdb5xob/pdb
• Related: 6AGG
• Descriptor: tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS, ZINC ION, MAGNESIUM ION (3 entities in total)
• Functional Keywords: zinc ribbon, conformational change, tias, trna modification, zinc finger engineering, ligase
• Biological source: Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
• Total number of polymer chains: 1
• Total formula weight: 48462.15

Authors

Dong, J. (deposition date: 2017-05-27, release date: 2018-08-29, Last modification date: 2024-10-23)

Primary citation

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., 430:4183-4194, 2018

PubMed Abstract: The accurate modification of the tRNA anticodon wobble cytosine 34 is critical for AUA decoding in protein synthesis. Archaeal tRNA cytosine 34 is modified with agmatine in the presence of ATP by TiaS (tRNA agmatidine synthetase). However, 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-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 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.

PubMed: 30121296
DOI: 10.1016/j.jmb.2018.08.015

Experimental method

X-RAY DIFFRACTION (2.48 Å)