2026-10-21 東京大学
非リボソームペプチド合成酵素 SacC の立体構造解明
＜関連情報＞
- https://www.s.u-tokyo.ac.jp/ja/press/11255/
- https://pubs.acs.org/jacsat/article-abstract/doi/10.1021/jacs.6c09555/5454651/Cryo-EM-Structure-of-a-Monomeric-Safracin-B
MbtH様タンパク質と共有結合プローブ捕捉によって可能になったモノマー型サフラシンB非リボソームペプチド合成酵素のクライオ電子顕微鏡構造 Cryo-EM Structure of a Monomeric Safracin B Nonribosomal Peptide Synthetase Enabled by an MbtH-like Protein and Covalent Probe Trapping
Naoto Haraguchi;Kanami Takahashi;Kana Matsuda;Kiichi Honda;Ryo Tanifuji;Takashi Matsui;Takeshi Yokoyama;Christos Gatsogiannis;Yoshikazu Tanaka;Hiroki Oguri
Journal of the American Chemical Society Published:October 20, 2026
DOI:https://doi.org/10.1021/jacs.6c09555
Abstract
Nonribosomal peptide synthetases (NRPSs) assemble structurally complex natural products but remain challenging targets for high-resolution structural analysis because of their conformational heterogeneity and dynamic catalytic cycles. SacC/SfmC is an unusual single-module NRPS that diverges from canonical peptide-forming assembly lines and instead catalyzes two sequential Pictet–Spengler reactions between a tyrosine-derived unit and a peptidyl aldehyde generated through thioester reduction. This cascade forms two C–C bonds, stereoselectively installs multiple stereogenic centers, and constructs the pentacyclic scaffold of bis-tetrahydroisoquinoline antitumor alkaloids including safracin B and the clinically important ecteinascidins. Here, we establish a state-resolved cryo-electron microscopy (cryo-EM) strategy for structural interrogation of the monomeric noncanonical NRPS SacC and report its thioesterification-state structure at 2.76 Å resolution. Stabilization of this transient catalytic state was achieved by combining the cognate MbtH-like partner protein with a tailored covalent adenosine vinylsulfonamide probe that mimics the aminoacyl-adenylate intermediate and traps the phosphopantetheine-tethered species within the adenylation domain. The structure directly visualizes a carrier protein-tethered intermediate and reveals the spatial organization of the Pictet–Spengler, adenylation, peptidyl carrier protein, and reduction domains, providing the first structural view of a Pictet–Spengler cyclization domain embedded within an NRPS assembly line. In parallel, nonreducible ester probes corresponding to downstream PCP-bound intermediates were developed to enable structural interrogation of additional catalytic states along the SacC reaction trajectory. These results demonstrate that rational chemical probe design enables state-resolved cryo-EM analysis of highly dynamic, single-module NRPSs and establishes a general strategy for capturing catalytic trajectories and enabling the engineering of noncanonical NRPS reactivity.
