1IRX

Crystal structure of class I lysyl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.

Terada, T.Nureki, O.Ishitani, R.Ambrogelly, A.Ibba, M.Soll, D.Yokoyama, S.

(2002) Nat.Struct.Mol.Biol. 9: 257-262

  • DOI: 10.1038/nsb777

  • PubMed Abstract: 
  • Lysyl-tRNA can be synthesized by both a class I (LysRS-I) and a class II (LysRS-II) lysyl-tRNA synthetase. The crystal structure of LysRS-I from Pyrococcus horikoshii at 2.6 A resolution reveals extensive similarity with glutamyl-tRNA synthetase (Glu ...

    Lysyl-tRNA can be synthesized by both a class I (LysRS-I) and a class II (LysRS-II) lysyl-tRNA synthetase. The crystal structure of LysRS-I from Pyrococcus horikoshii at 2.6 A resolution reveals extensive similarity with glutamyl-tRNA synthetase (GluRS). A comparison of the structures of LysRS-I and LysRS-II in complex with lysine shows that both enzymes use similar strategies for substrate recognition within unrelated active site topologies. A docking model based upon the GluRS-tRNA complex suggests how LysRS-I and LysRS-II can recognize the same molecular determinants in tRNALys, as shown by biochemical results, while approaching the acceptor helix of the tRNA from opposite sides.


    Organizational Affiliation

    RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lysyl-tRNA synthetase
A, B
523Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Gene Names: lysS
EC: 6.1.1.6
Find proteins for O57963 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O57963
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.945α = 90.00
b = 74.767β = 90.26
c = 156.945γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance