5XOB

Crystal structure of apo TiaS (tRNAIle2 agmatidine synthetase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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.

(2018) J Mol Biol 430: 4183-4194

  • DOI: 10.1016/j.jmb.2018.08.015
  • Primary Citation of Related Structures:  
    5XOB, 6AGG

  • PubMed Abstract: 
  • 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 ...

    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). 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 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.


    Organizational Affiliation

    Hefei National Laboratory for Physical Science at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China; Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: wgong@ustc.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA(Ile2) 2-agmatinylcytidine synthetase TiaSZ420Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: tiaSAF_2259
EC: 6.3.4.22
Find proteins for O28025 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28025 
Go to UniProtKB:  O28025
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
Z
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
ZL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.926α = 90
b = 68.926β = 90
c = 211.102γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-27 
  • Released Date: 2018-08-29 
  • Deposition Author(s): Dong, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-24
    Changes: Data collection, Database references