4J15

Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex

Kim, K.R.Park, S.H.Kim, H.S.Rhee, K.H.Kim, B.-G.Kim, D.G.Park, M.S.Kim, H.-J.Kim, S.Han, B.W.

(2013) Proteins 81: 1840-1846

  • DOI: 10.1002/prot.24306

  • PubMed Abstract: 
  • Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling p ...

    Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at a resolution of 2.25 Å. DRS is a homodimer with a dimer interface of 3750.5 Å(2) which comprises 16.6% of the monomeric surface area. Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNA(Asp) to elongation factor 1α. From our analyses of the crystal structure and post-translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions.


    Organizational Affiliation

    Research Institute of Pharmaceutical Sciences, Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate--tRNA ligase, cytoplasmic
A, B
521Homo sapiensMutation(s): 0 
Gene Names: DARS
EC: 6.1.1.12
Find proteins for P14868 (Homo sapiens)
Go to Gene View: DARS
Go to UniProtKB:  P14868
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, 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: 2.24 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.885α = 90.00
b = 141.921β = 102.19
c = 68.495γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references