1LYL

LYSYL-TRNA SYNTHETASE (LYSU) (E.C.6.1.1.6) COMPLEXED WITH LYSINE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli

Onesti, S., Miller, A.D., Brick, P.

(1995) Structure 3: 163-176

  • DOI: 10.1016/s0969-2126(01)00147-2
  • Primary Citation of Related Structures:  
    1LYL

  • PubMed Abstract: 

    • Lysyl-tRNA synthetase catalyzes the attachment of the amino acid lysine to the cognate tRNA. The enzyme is a member of the class II amino-acyl-tRNA synthetases; the crystal structures of the seryl- and aspartyl-tRNA synthetases from this class are already known ...

    Lysyl-tRNA synthetase catalyzes the attachment of the amino acid lysine to the cognate tRNA. The enzyme is a member of the class II amino-acyl-tRNA synthetases; the crystal structures of the seryl- and aspartyl-tRNA synthetases from this class are already known. Lysyl-tRNA synthetase shows extensive sequence homology with aspartyl-tRNA synthetase. In Escherichia coli there are two isoforms of the enzyme, LysS and LysU. Unlike LysS, which is synthesized under normal growth conditions, LysU is the product of a normally silent gene which is overexpressed under extreme physiological conditions (such as heat-shock), and can synthesize a number of adenyl dinucleotides (in particular AppppA). These dinucleotides have been proposed to act as modulators of the heat-shock response and stress response.

    Related Citations: 
    • Crystallization and Preliminary Diffraction Studies of E.Coli Lysyl-T(Slash)RNA Synthetase (Lysu)
      Onesti, S., Theoclitou, M.-E., Wittung, E.P.L., Miller, A.D., Plateau, P., Blanquet, S., Brick, P.
      (1994) J Mol Biol 243: 123
    Organizational Affiliation: 

    Blackett Laboratory, Imperial College, London, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSYL-TRNA SYNTHETASE (LYSU)A, B, C504Escherichia coliMutation(s): 0 
EC: 6.1.1.6
UniProt
Find proteins for P0A8N5 (Escherichia coli (strain K12))
Explore P0A8N5 
Go to UniProtKB:  P0A8N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8N5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.27α = 90
b = 257.8β = 90
c = 182.08γ = 90
Software Package:
Software NamePurpose
MOSFLM/CCP4data collection
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data reduction
X-PLORphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 1995-05-03 
  • Released Date: 1995-10-15 
    • Deposition Author(s): Onesti, S., Brick, P.

Revision History  (Full details and data files)

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance