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 1.1 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: 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) ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate--tRNA ligase, cytoplasmicA, B, G, H502Homo sapiensMutation(s): 0 
Gene Names: DARSPIG40DARS1
EC: 6.1.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for P14868 (Homo sapiens)
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Go to UniProtKB:  P14868
PHAROS:  P14868
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2C, D, I, J215Homo sapiensMutation(s): 0 
Gene Names: AIMP2JTV1PRO0992
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Find proteins for Q13155 (Homo sapiens)
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PHAROS:  Q13155
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional glutamate/proline--tRNA ligaseE, F, K, L165Homo sapiensMutation(s): 0 
Gene Names: EPRSGLNSPARSQARSQPRSPIG32EPRS1
EC: 6.1.1.17 (PDB Primary Data), 6.1.1.15 (PDB Primary Data)
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Find proteins for P07814 (Homo sapiens)
Explore P07814 
Go to UniProtKB:  P07814
PHAROS:  P07814
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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] , O [auth A] , P [auth A] , Q [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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth H], M [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



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