6SPR

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

Summary for 6SPR

• Entry DOI: 10.2210/pdb6spr/pdb
• Related: 1QQT
• Descriptor: Methionine--tRNA ligase, ZINC ION, (3R)-3-amino-5-(methylsulfanyl)pentanoic acid, ... (6 entities in total)
• Functional Keywords: trna aminoacylation, translation
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 65725.30

Authors

Nigro, G.,Schmitt, E.,Mechulam, Y. (deposition date: 2019-09-02, release date: 2020-01-01, Last modification date: 2024-01-24)

Primary citation

Nigro, G.,Bourcier, S.,Lazennec-Schurdevin, C.,Schmitt, E.,Marliere, P.,Mechulam, Y.
Use of beta3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase.
J.Struct.Biol., 209:107435-107435, 2020

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-Met by Escherichia coli methionyl-tRNA synthetase (MetRS). We show that MetRS binds β-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-Met commercial samples. The 1.45 Å crystal structure of the MetRS: β-Met complex shows that β-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-Met aminoacylation capabilities.

PubMed: 31862305
DOI: 10.1016/j.jsb.2019.107435

Experimental method

X-RAY DIFFRACTION (1.48 Å)