3H9B

Structure of a mutant methionyl-tRNA synthetase with modified specificity complexed with azidonorleucine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Switching from an induced-fit to a lock-and-key mechanism in an aminoacyl-tRNA synthetase with modified specificity.

Schmitt, E.Tanrikulu, I.C.Yoo, T.H.Panvert, M.Tirrell, D.A.Mechulam, Y.

(2009) J.Mol.Biol. 394: 843-851

  • DOI: 10.1016/j.jmb.2009.10.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionyl-tRNA synthetase (MetRS) specifically binds its methionine substrate in an induced-fit mechanism, with methionine binding causing large rearrangements. Mutated MetRS able to efficiently aminoacylate the methionine (Met) analog azidonorleucin ...

    Methionyl-tRNA synthetase (MetRS) specifically binds its methionine substrate in an induced-fit mechanism, with methionine binding causing large rearrangements. Mutated MetRS able to efficiently aminoacylate the methionine (Met) analog azidonorleucine (Anl) have been identified by saturation mutagenesis combined with in vivo screening procedures. Here, the crystal structure of such a mutated MetRS was determined in the apo form as well as complexed with Met or Anl (1.4 to 1.7 A resolution) to reveal the structural basis for the altered specificity. The mutations result in both the loss of important contacts with Met and the creation of new contacts with Anl, thereby explaining the specificity shift. Surprisingly, the conformation induced by Met binding in wild-type MetRS already occurs in the apo form of the mutant enzyme. Therefore, the mutations cause the enzyme to switch from an induced-fit mechanism to a lock-and-key one, thereby enhancing its catalytic efficiency.


    Organizational Affiliation

    Ecole Polytechnique, Laboratoire de Biochimie, F-91128 Palaiseau Cedex, France; CNRS, UMR7654, Laboratoire de Biochimie, Ecole Polytechnique, F-91128 Palaiseau Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionyl-tRNA synthetase
A
560Escherichia coli (strain K12)Mutation(s): 3 
Gene Names: metG
EC: 6.1.1.10
Find proteins for P00959 (Escherichia coli (strain K12))
Go to UniProtKB:  P00959
Small Molecules
Ligands 3 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
CIT
Query on CIT

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Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NOT
Query on NOT

Download SDF File 
Download CCD File 
A
6-azido-L-norleucine
AZIDONORLEUCINE
C6 H12 N4 O2
HTFFMYRVHHNNBE-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.259α = 90.00
b = 45.377β = 107.24
c = 85.890γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XSCALEdata scaling
CNSrefinement
CNSphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance