EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.
ジャーナル・号・ページ	ACS Cent Sci, Vol. 9, Issue 6, Page 1160-1169, Year 2023
掲載日	2023年6月28日
著者	Chandrima Majumdar / Joshua A Walker / Matthew B Francis / Alanna Schepartz / Jamie H D Cate /
PubMed 要旨	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 ...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.
リンク	ACS Cent Sci / PubMed:37396857 / PubMed Central
手法	EM (単粒子)
解像度	2.02 - 2.31 Å
構造データ	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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 2.09 Å EMDB-29790: 30S focus refined map of WT E.coli ribosome complexed with A-site ortho-aminobenzoic acid charged tRNA-Phe 手法: EM (単粒子) / 解像度: 2.14 Å
化合物	ChemComp-ZN: Unknown entry ChemComp-PAR: PAROMOMYCIN / パロモマイシン / Antimicrobial, 薬剤YM / パロモマイシン ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-2AE: 2-AMINO-BENZAMIDE / 2-アミノベンズアミド ChemComp-8AN: 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate) / 3′-アミノ-3′-デオキシアデノシン5′-りん酸 ChemComp-FME: N-FORMYLMETHIONINE / N-ホルミルメチオニン / N-ホルミルメチオニン ChemComp-K: Unknown entry / カリウムカチオン ChemComp-SPD: SPERMIDINE / スペルミジン / スペルミジン ChemComp-HOH: WATER / 水 ChemComp-SPM: SPERMINE / スペルミン / スペルミン ChemComp-3AB: 3-aminobenzamide / 3-アミノベンズアミド / 3-Aminobenzamide ChemComp-YRW*: 3-aminopyridine-4-carboxamide
由来	escherichia coli (大腸菌)
キーワード	RIBOSOME (リボソーム) / non-natural monomers / aminobenzoic acids / unnatural monomers