9I5M

Structure of cyclodipeptide synthase from Nocardia brasiliensis (Nbra-CDPS)

9I5M の概要

• エントリーDOI: 10.2210/pdb9i5m/pdb
• 関連するPDBエントリー: 5MLQ
• 分子名称: Cyclodipeptide synthase, PHOSPHATE ION (3 entities in total)
• 機能のキーワード: nonribosomal peptide synthetases cyclodipeptide synthases ligase, rna binding protein
• 由来する生物種: Nocardia brasiliensis ATCC 700358
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 55267.05

構造登録者

Marouf, F.Z.,Charbonnier, J.B.,Fernandez Varela, P. (登録日: 2025-01-28, 公開日: 2026-02-18, 最終更新日: 2026-04-22)

主引用文献

Marouf, Z.,Tellier-Lebegue, C.,Glousieau, M.,Morellet, N.,Cuniasse, P.,Bourand-Plantefol, A.,Plancqueel, S.,Mahmoudi, I.,Andreani, J.,Legrand, P.,Ropars, V.,Ruedas, R.,Hermouet, L.F.,Moutiez, M.,Nhiri, N.,Fonvielle, M.,Bressanelli, S.,Katoh, T.,Fernandez Varela, P.,Lescop, E.,Charbonnier, J.B.,Gondry, M.
The tRNA moieties of both aminoacyl-tRNA substrates of a cyclodipeptide synthase share a common binding site, as revealed by RNA microhelices mimicking tRNA acceptor arms.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: Cyclodipeptide synthases (CDPSs) sequentially use two aminoacyl-tRNAs (AA-tRNAs) as substrates to catalyze cyclodipeptide formation. We previously showed that microhelices (miHxs), which mimic the tRNAs acceptor arms, are as efficient as full-length AA-tRNAs as substrates when aminoacylated by flexizymes. We generated a diverse set of miHxs (acylated, unacylated, misacylated, mutated, or shortened miHxs) and analyzed their interactions with CDPSs. We studied the Nocardia brasiliensis CDPS (Nbra-CDPS), which synthesizes cyclo(l-Ala-l-Glu) using Ala-tRNAAla and Glu-tRNAGlu as its first and second substrates, respectively. We determined the crystal structure of Nbra-CDPS bound to two analogues of its first substrate, unacylated miHxAla and acylated miHxAla, in which alanine is attached via an amide bond. We showed by cryoEM that the miHxAla mimics well the acceptor stem of the full-length tRNAAla. We determined the crystal structure of Nbra-CDPS bound to unacylated miHxGlu, an analogue of its second substrate, and showed that, despite sequence differences, it superimposes well with miHxAla. This result, combined with the use of misacylated substrates, indicates that the RNA stem moieties of both substrates share a common binding mode. Together, our findings establish miHxs as powerful tools for dissecting CDPS substrate recognition and provide a framework for studying other AA-tRNA-utilizing enzymes.

PubMed: 41954980
DOI: 10.1093/nar/gkag307

実験手法

X-RAY DIFFRACTION (1.734 Å)