1BBU

LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE

• PDB DOI: https://doi.org/10.2210/pdb1BBU/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-04-24 Released: 2000-11-10 
• Deposition Author(s): Onesti, S., Desogus, G., Brevet, A., Chen, J., Plateau, P., Blanquet, S., Brick, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.297 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.

Onesti, S., Desogus, G., Brevet, A., Chen, J., Plateau, P., Blanquet, S., Brick, P.

(2000) Biochemistry 39: 12853-12861

• PubMed: 11041850 
• DOI: https://doi.org/10.1021/bi001487r
• Primary Citation of Related Structures:  
  1BBU, 1BBW


• PubMed Abstract: 
  

  Lysyl-tRNA synthetase is a member of the class II aminoacyl-tRNA synthetases and catalyses the specific aminoacylation of tRNA(Lys). The crystal structure of the constitutive lysyl-tRNA synthetase (LysS) from Escherichia coli has been determined to 2.7 A resolution in the unliganded form and in a complex with the lysine substrate. A comparison between the unliganded and lysine-bound structures reveals major conformational changes upon lysine binding. The lysine substrate is involved in a network of hydrogen bonds. Two of these interactions, one between the alpha-amino group and the carbonyl oxygen of Gly 216 and the other between the carboxylate group and the side chain of Arg 262, trigger a subtle and complicated reorganization of the active site, involving the ordering of two loops (residues 215-217 and 444-455), a change in conformation of residues 393-409, and a rotation of a 4-helix bundle domain (located between motif 2 and 3) by 10 degrees. The result of these changes is a closing up of the active site upon lysine binding.

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Organizational Affiliation: 

Biophysics Section, Blackett Laboratory, Imperial College, London SW7 2BZ, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 57.69 kDa 
• Atom Count: 3,950 
• Modelled Residue Count: 486 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (LYSYL-TRNA SYNTHETASE)	A	504	Escherichia coli K-12	Mutation(s): 0  Gene Names: LYSS EC: 6.1.1.6
UniProt
Find proteins for P0A8N3 (Escherichia coli (strain K12)) Explore P0A8N3  Go to UniProtKB:  P0A8N3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	B [auth A]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.297 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.82	α = 90
b = 181.82	β = 90
c = 93.07	γ = 120

Software Package:

Software Name	Purpose
CCP4	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-10 
Deposition Author(s): Onesti, S., Desogus, G., Brevet, A., Chen, J., Plateau, P., Blanquet, S., Brick, P.

Revision History  

• Version 1.0: 2000-11-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description