6SPR

Structure of the Escherichia coli methionyl-tRNA synthetase variant VI298 complexed with beta-methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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.

(2020) J Struct Biol 209: 107435-107435

  • DOI: https://doi.org/10.1016/j.jsb.2019.107435
  • Primary Citation of Related Structures:  
    6SPN, 6SPO, 6SPP, 6SPQ, 6SPR

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine--tRNA ligase568Escherichia coliMutation(s): 1 
Gene Names: metGb2114JW2101
EC: 6.1.1.10
UniProt
Find proteins for P00959 (Escherichia coli (strain K12))
Explore P00959 
Go to UniProtKB:  P00959
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00959
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
B3M (Subject of Investigation/LOI)
Query on B3M

Download Ideal Coordinates CCD File 
C [auth A](3R)-3-amino-5-(methylsulfanyl)pentanoic acid
C6 H13 N O2 S
QWVNCDVONVDGDV-YFKPBYRVSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.31α = 90
b = 45.11β = 107.39
c = 86.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2024-01-24
    Changes: Refinement description