4DPG

Crystal Structure of Human LysRS: P38/AIMP2 Complex I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription.

Ofir-Birin, Y.Fang, P.Bennett, S.P.Zhang, H.M.Wang, J.Rachmin, I.Shapiro, R.Song, J.Dagan, A.Pozo, J.Kim, S.Marshall, A.G.Schimmel, P.Yang, X.L.Nechushtan, H.Razin, E.Guo, M.

(2013) Mol Cell 49: 30-42

  • DOI: 10.1016/j.molcel.2012.10.010
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Lysyl-tRNA synthetase (LysRS), a component of the translation apparatus, is released from the cytoplasmic multi-tRNA synthetase complex (MSC) to activate the transcription factor MITF in stimulated mast cells through undefined mechanisms. Here we sho ...

    Lysyl-tRNA synthetase (LysRS), a component of the translation apparatus, is released from the cytoplasmic multi-tRNA synthetase complex (MSC) to activate the transcription factor MITF in stimulated mast cells through undefined mechanisms. Here we show that Ser207 phosphorylation provokes a new conformer of LysRS that inactivates its translational function but activates its transcriptional function. The crystal structure of an MSC subcomplex established that LysRS is held in the MSC by binding to the N terminus of the scaffold protein p38/AIMP2. Phosphorylation-created steric clashes at the LysRS domain interface disrupt its binding grooves for p38/AIMP2, releasing LysRS and provoking its nuclear translocation. This alteration also exposes the C-terminal domain of LysRS to bind to MITF and triggers LysRS-directed production of the second messenger Ap(4)A that activates MITF. Thus our results establish that a single conformational change triggered by phosphorylation leads to multiple effects driving an exclusive switch of LysRS function from translation to transcription.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine--tRNA ligase
A, B, C, D, E, F, G, H
513Homo sapiensMutation(s): 0 
Gene Names: KARSKIAA0070KARS1
EC: 6.1.1.6 (PDB Primary Data), 2.7.7 (UniProt)
Find proteins for Q15046 (Homo sapiens)
Go to UniProtKB:  Q15046
NIH Common Fund Data Resources
PHAROS  Q15046

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
I, J, K, L
54Homo sapiensMutation(s): 0 
Gene Names: AIMP2JTV1PRO0992
Find proteins for Q13155 (Homo sapiens)
Go to UniProtKB:  Q13155
NIH Common Fund Data Resources
PHAROS  Q13155
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download CCD File 
A, B, C, D, E, F, G, H
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
LYS
Query on LYS

Download CCD File 
A, B, C, D, E, F, G, H
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
ALA
Query on ALA

Download CCD File 
H
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, F, G, H, J, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.2α = 89.16
b = 122.01β = 85.58
c = 149.2γ = 89.71
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description