5H34

Crystal structure of the C-terminal domain of methionyl-tRNA synthetase (MetRS-C) in Nanoarchaeum equitans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.748 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans.

Suzuki, H.Kaneko, A.Yamamoto, T.Nambo, M.Hirasawa, I.Umehara, T.Yoshida, H.Park, S.Y.Tamura, K.

(2017) J. Mol. Evol. 84: 267-278

  • DOI: 10.1007/s00239-017-9796-6

  • PubMed Abstract: 
  • The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as ...

    The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligosaccharide-binding fold (OB-fold). Analysis using a quartz crystal microbalance indicated that MetRS-C freshly isolated from N. equitans was bound to tRNA. However, binding of the split 3'-half tRNA species was stronger than that of the 5'-half species. The T-loop and the 3'-end regions of the split 3'-half tRNA were found to be responsible for the binding. The minimum structure for binding to MetRS-C might be a minihelix-like stem-loop with single-stranded 3'-terminus. After successive duplications of such a small hairpin structure with the assistance of a Trbp-like structure, the interaction of the T-loop region of the 3'-half with a Trbp-like structure could have been evolutionarily replaced by RNA-RNA interactions, along with many combinational tertiary interactions, to form the modern tRNA structure.


    Organizational Affiliation

    Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine-tRNA ligase
A, B
135Nanoarchaeum equitans (strain Kin4-M)Mutation(s): 0 
Gene Names: metG
EC: 6.1.1.10
Find proteins for Q74MZ1 (Nanoarchaeum equitans (strain Kin4-M))
Go to UniProtKB:  Q74MZ1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.748 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.638α = 90.00
b = 58.824β = 90.00
c = 59.487γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references