6SPO

Structure of the Escherichia coli methionyl-tRNA synthetase complexed with methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Use of beta3-methionine as an amino acid substrate of Escherichia coli Methionyl-tRNA synthetase.

Nigro, G.Bourcier, S.Lazennec-Schurdevin, C.Schmitt, E.Marliere, P.Mechulam, Y.

(2019) J.Struct.Biol. --: 107435-107435

  • DOI: 10.1016/j.jsb.2019.107435
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polypeptides containing β-amino acids are attractive tools for the design of novel proteins having unique properties of medical or industrial interest. Incorporation of β-amino acids in vivo requires the development of efficient aminoacyl-tRNA synthe ...

    Polypeptides containing β-amino acids are attractive tools for the design of novel proteins having unique properties of medical or industrial interest. Incorporation of β-amino acids in vivo requires the development of efficient aminoacyl-tRNA synthetases specific of these non-canonical amino acids. Here, we have performed a detailed structural and biochemical study of the recognition and use of β 3 -Met by Escherichia coli methionyl-tRNA synthetase (MetRS). We show that MetRS binds β 3 -Met with a 24-fold lower affinity but catalyzes the esterification of the non-canonical amino acid onto tRNA with a rate lowered by three orders of magnitude. Accurate measurements of the catalytic parameters required careful consideration of the presence of contaminating α-Met in β 3 -Met commercial samples. The 1.45 Å crystal structure of the MetRS: β 3 -Met complex shows that β 3 -Met binds the enzyme essentially like α-Met, but the carboxylate moiety is mobile and not adequately positioned to react with ATP for aminoacyl adenylate formation. This study provides structural and biochemical bases for engineering MetRS with improved β 3 -Met aminoacylation capabilities.


    Organizational Affiliation

    Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France. Electronic address: emmanuelle.schmitt@polytechnique.edu.,Laboratoire de Chimie Moléculaire, LCM, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France.,Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France. Electronic address: yves.mechulam@polytechnique.edu.,Xenome Research Group, Institute of Systems and Synthetic Biology, CNRS, UMR8030, UEVE, CEA, GENOPOLE, 5 rue Henri Desbruères, 91030 Evry Cedex, France.,Laboratoire de Biochimie, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine--tRNA ligase
A
568Escherichia coliMutation(s): 0 
Gene Names: metG
EC: 6.1.1.10
Find proteins for A0A0F3U9S7 (Escherichia coli)
Go to UniProtKB:  A0A0F3U9S7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

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Download CCD File 
A
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.290α = 90.00
b = 45.190β = 107.39
c = 85.890γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release