1H3N

Leucyl-tRNA synthetase from Thermus thermophilus complexed with a sulphamoyl analogue of leucyl-adenylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2A Structure of Leucyl-tRNA Synthetase and its Complex with a Leucyl-Adenylate Analogue

Cusack, S.Yaremchuk, A.Tukalo, M.

(2000) Embo J. 19: 2351

  • DOI: 10.1093/emboj/19.10.2351
  • Also Cited By: 1OBH, 1OBC

  • PubMed Abstract: 
  • Leucyl-, isoleucyl- and valyl-tRNA synthetases are closely related large monomeric class I synthetases. Each contains a homologous insertion domain of approximately 200 residues, which is thought to permit them to hydrolyse ('edit') cognate tRNA that ...

    Leucyl-, isoleucyl- and valyl-tRNA synthetases are closely related large monomeric class I synthetases. Each contains a homologous insertion domain of approximately 200 residues, which is thought to permit them to hydrolyse ('edit') cognate tRNA that has been mischarged with a chemically similar but non-cognate amino acid. We describe the first crystal structure of a leucyl-tRNA synthetase, from the hyperthermophile Thermus thermophilus, at 2.0 A resolution. The overall architecture is similar to that of isoleucyl-tRNA synthetase, except that the putative editing domain is inserted at a different position in the primary structure. This feature is unique to prokaryote-like leucyl-tRNA synthetases, as is the presence of a novel additional flexibly inserted domain. Comparison of native enzyme and complexes with leucine and a leucyl- adenylate analogue shows that binding of the adenosine moiety of leucyl-adenylate causes significant conformational changes in the active site required for amino acid activation and tight binding of the adenylate. These changes are propagated to more distant regions of the enzyme, leading to a significantly more ordered structure ready for the subsequent aminoacylation and/or editing steps.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of Thermus Thermophilus Leucyl-tRNA Synthetase and its Complexes with Leucine and a Non-Hydrolysable Leucyl-Adenylate Analogue
      Yaremchuk, A.,Cusack, S.,Gudzera, O.,Grotli, M.,Tukalo, M.
      (2000) Acta Crystallogr.,Sect.D 56: 667


    Organizational Affiliation

    European Molecular Laboratory Biology, Grenoble outstation, c/o ILL, 156X, F-38042 Grenoble, Cedex 9, France. cusack@embl-grenoble.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LEUCYL-TRNA SYNTHETASE
A
878Thermus thermophilusGene Names: leuS
EC: 6.1.1.4
Find proteins for Q7SIE4 (Thermus thermophilus)
Go to UniProtKB:  Q7SIE4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LMS
Query on LMS

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Download CCD File 
A
[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE
C10 H14 N6 O6 S
GNZLUJQJDPRUTD-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LEU
Query on LEU

Download SDF File 
Download CCD File 
A
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 102.410α = 90.00
b = 155.590β = 90.00
c = 176.300γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance