6IY6

Crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with glutathion-S transferase (GST) domains from Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (EPRS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The DRS-AIMP2-EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex.

Hahn, H., Park, S.H., Kim, H.J., Kim, S., Han, B.W.

(2019) IUCrJ 6: 958-967

  • DOI: https://doi.org/10.1107/S2052252519010790
  • Primary Citation of Related Structures:  
    6IY6

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases (ARSs) play essential roles in protein biosynthesis as well as in other cellular processes, often using evolutionarily acquired domains. For possible cooperativity and synergistic effects, nine ARSs assemble into the multi-tRNA synthetase complex (MSC) with three scaffold proteins: aminoacyl-tRNA synthetase complex-interacting multifunctional proteins 1, 2 and 3 (AIMP1, AIMP2 and AIMP3). X-ray crystallographic methods were implemented in order to determine the structure of a ternary subcomplex of the MSC comprising aspartyl-tRNA synthetase (DRS) and two glutathione S -transferase (GST) domains from AIMP2 and glutamyl-prolyl-tRNA synthetase (AIMP2 GST and EPRS GST , respectively). While AIMP2 GST and EPRS GST interact via conventional GST heterodimerization, DRS strongly interacts with AIMP2 GST via hydrogen bonds between the α7-β9 loop of DRS and the β2-α2 loop of AIMP2 GST , where Ser156 of AIMP2 GST is essential for the assembly. Structural analyses of DRS-AIMP2 GST -EPRS GST reveal its pivotal architecture in the MSC and provide valuable insights into the overall assembly and conditionally required disassembly of the MSC.

    • Organizational Affiliation: 

    Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate--tRNA ligase, cytoplasmic
A, B, G, H
502Homo sapiensMutation(s): 0 
Gene Names: DARS, PIG40
EC: 6.1.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for P14868 (Homo sapiens)
Explore P14868 
Go to UniProtKB:  P14868
PHAROS:  P14868
GTEx:  ENSG00000115866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14868
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
C, D, I, J
215Homo sapiensMutation(s): 0 
Gene Names: AIMP2, JTV1, PRO0992
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens)
Explore Q13155 
Go to UniProtKB:  Q13155
PHAROS:  Q13155
GTEx:  ENSG00000106305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13155
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional glutamate/proline--tRNA ligase
E, F, K, L
165Homo sapiensMutation(s): 0 
Gene Names: EPRS, GLNS, PARS, QARS, QPRS, PIG32
EC: 6.1.1.17 (PDB Primary Data), 6.1.1.15 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P07814 (Homo sapiens)
Explore P07814 
Go to UniProtKB:  P07814
PHAROS:  P07814
GTEx:  ENSG00000136628 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07814
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
DA [auth H]
EA [auth H]
N [auth A]
AA [auth G],
BA [auth G],
DA [auth H],
EA [auth H],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth G]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CA [auth H],
M [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.068α = 90
b = 108.068β = 90
c = 815.642γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2011-0030001
National Research Foundation (Korea)Korea, Republic OfNRF-2013M-3A6A-4043695

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description