1IRX

Crystal structure of class I lysyl-tRNA synthetase

• PDB DOI: https://doi.org/10.2210/pdb1IRX/pdb

• Classification: LIGASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-10-25 Released: 2002-04-17 
• Deposition Author(s): Nureki, O., Terada, T., Ishitani, R., Ambrogelly, A., Ibba, M., Soll, D., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.292 
• R-Value Work: 0.225 

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 Biol 9: 257-262

• PubMed: 11887185 
• DOI: https://doi.org/10.1038/nsb777
• Primary Citation of Related Structures:  
  1IRX


• 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 (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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 123.57 kDa 
• Atom Count: 8,754 
• Modelled Residue Count: 1,015 
• Deposited Residue Count: 1,046 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lysyl-tRNA synthetase	A, B	523	Pyrococcus horikoshii	Mutation(s): 0  EC: 6.1.1.6
UniProt
Find proteins for O57963 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57963  Go to UniProtKB:  O57963

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.292 
• R-Value Work: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.945	α = 90
b = 74.767	β = 90.26
c = 156.945	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-17 
Deposition Author(s): Nureki, O., Terada, T., Ishitani, R., Ambrogelly, A., Ibba, M., Soll, D., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2002-04-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations