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TitleAminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.
Journal, issue, pagesACS Cent Sci, Vol. 9, Issue 6, Page 1160-1169, Year 2023
Publish dateJun 28, 2023
AuthorsChandrima Majumdar / Joshua A Walker / Matthew B Francis / Alanna Schepartz / Jamie H D Cate /
PubMed AbstractThe () ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no ...The () ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), aminobenzoic acid (ABZ), and aminobenzoic acid (ABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by ABZ and then ABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.
External linksACS Cent Sci / PubMed:37396857 / PubMed Central
MethodsEM (single particle)
Resolution2.02 - 2.31 Å
Structure data

29786

8g6w

EMDB-29786, PDB-8g6w:
Structure of WT E.coli 70S ribosome complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site ortho-aminobenzoic acid charged NH-tRNAPhe
Method: EM (single particle) / Resolution: 2.02 Å

29787

8g6x

EMDB-29787, PDB-8g6x:
Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site meta-aminobenzoic acid charged NH-tRNAPhe
Method: EM (single particle) / Resolution: 2.31 Å

29788

8g6y

EMDB-29788, PDB-8g6y:
Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site 3-aminopyridine-4-carboxylic acid charged NH-tRNAPhe
Method: EM (single particle) / Resolution: 2.09 Å

EMDB-29790: 30S focus refined map of WT E.coli ribosome complexed with A-site ortho-aminobenzoic acid charged tRNA-Phe
Method: EM (single particle) / Resolution: 2.14 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-PAR:
PAROMOMYCIN / Antimicrobial, medication*YM / Paromomycin

ChemComp-MG:
Unknown entry

ChemComp-2AE:
2-AMINO-BENZAMIDE

ChemComp-8AN:
3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)

ChemComp-FME:
N-FORMYLMETHIONINE / N-Formylmethionine

ChemComp-K:
Unknown entry

ChemComp-SPD:
SPERMIDINE / Spermidine

ChemComp-HOH:
WATER / Water

ChemComp-SPM:
SPERMINE / Spermine

ChemComp-3AB:
3-aminobenzamide / 3-Aminobenzamide

ChemComp-YRW:
3-aminopyridine-4-carboxamide

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / non-natural monomers / aminobenzoic acids / unnatural monomers

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