7U0R

Crystal structure of Methanomethylophilus alvus PylRS(N166A/V168A) complexed with meta-trifluoromethyl-2-benzylmalonate and AMP-PNP

Summary for 7U0R

• Entry DOI: 10.2210/pdb7u0r/pdb
• Descriptor: Pyrrolysyl-tRNA synthetase, {[3-(trifluoromethyl)phenyl]methyl}propanedioic acid, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... (6 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, ligase, non-natural amino acids, pyrrolysyl-trna synthetase, translation, translation-inhibitor complex, translation/inhibitor
• Biological source: Candidatus Methanomethylophilus alvus
• Total number of polymer chains: 2
• Total formula weight: 63895.01

Authors

Swenson, C.V.,Roe, L.T.,Fricke, R.C.B.,Smaga, S.S.,Gee, C.L.,Schepartz, A. (deposition date: 2022-02-18, release date: 2023-06-14, Last modification date: 2023-10-25)

Primary citation

Fricke, R.,Swenson, C.V.,Roe, L.T.,Hamlish, N.X.,Shah, B.,Zhang, Z.,Ficaretta, E.,Ad, O.,Smaga, S.,Gee, C.L.,Chatterjee, A.,Schepartz, A.
Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-alpha-amino acids in vitro and in vivo.
Nat.Chem., 15:960-971, 2023

PubMed Abstract: The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.

PubMed: 37264106
DOI: 10.1038/s41557-023-01224-y

Experimental method

X-RAY DIFFRACTION (1.8 Å)