5A1N

The crystal structure of the GST-like domains complex of EPRS-AIMP2 mutant S156D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Symmetric Assembly of a Decameric Subcomplex in Human Multi-tRNA Synthetase Complex Via Interactions between Glutathione Transferase-Homology Domains and Aspartyl-tRNA Synthetase.

Cho, H.Y.Lee, H.J.Choi, Y.S.Kim, D.K.Jin, K.S.Kim, S.Kang, B.S.

(2019) J.Mol.Biol. --: --

  • DOI: 10.1016/j.jmb.2019.08.013

  • PubMed Abstract: 
  • Aminoacyl-tRNA synthetases (AARSs) ligate amino acids to their cognate tRNAs during protein synthesis. In humans, eight AARSs and three non-enzymatic AARS-interacting multifunctional proteins (AIMP1-3), which are involved in various biological proces ...

    Aminoacyl-tRNA synthetases (AARSs) ligate amino acids to their cognate tRNAs during protein synthesis. In humans, eight AARSs and three non-enzymatic AARS-interacting multifunctional proteins (AIMP1-3), which are involved in various biological processes, form a multi-tRNA synthetase complex (MSC). Elucidation of the structures and multiple functions of individual AARSs and AIMPs has aided current understanding of the structural arrangement of MSC components and their assembly processes. Here, we report the crystal structure of a complex comprising a motif from aspartyl-tRNA synthetase (DRS) and the glutathione transferase (GST)-homology domains of methionyl-tRNA synthetase (MRS), glutamyl-prolyl-tRNA synthetase (EPRS), AIMP2, and AIMP3. In the crystal structure, the four GST domains are assembled in the order of MRS-AIMP3-EPRS-AIMP2, and the GST domain of AIMP2 binds DRS through the β-sheet in the GST domain. The C-terminus of AIMP3 enhances the binding of DRS to the tetrameric GST complex. A DRS dimer and two GST tetramers binding to the dimer with 2-fold symmetry complete a decameric complex. The formation of this complex enhances the stability of DRS and enables it to retain its reaction intermediate, aspartyl adenylate. Since the catalytic domains of MRS and EPRS are connected to the decameric complex through their flexible linker peptides, and lysyl-tRNA synthetase and AIMP1 are also linked to the complex via the N-terminal region of AIMP2, the DRS-GST tetramer complex functions as a frame in the MSC.


    Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, 80 Jigokro-127-beongil, Nam-Gu, Pohang, Kyungbuk 37673, Republic of Korea.,Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea; College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea. Electronic address: bskang2@knu.ac.kr.,School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
A
175Homo sapiensMutation(s): 3 
Gene Names: EPRS (GLNS, PARS, QARS, QPRS)
Find proteins for P07814 (Homo sapiens)
Go to Gene View: EPRS
Go to UniProtKB:  P07814
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
B
240Homo sapiensMutation(s): 1 
Gene Names: AIMP2 (JTV1)
Find proteins for Q13155 (Homo sapiens)
Go to Gene View: AIMP2
Go to UniProtKB:  Q13155
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.619α = 90.00
b = 75.619β = 90.00
c = 175.819γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Database references