9VAR

Crystal structure of Cu-bound artificial metalloprotein incorporating a TP ligand

これはPDB形式変換不可エントリーです。

9VAR の概要

• エントリーDOI: 10.2210/pdb9var/pdb
• 分子名称: dTDP-4-dehydrorhamnose 3,5-epimerase, COPPER (II) ION, SODIUM ION, ... (5 entities in total)
• 機能のキーワード: noncanonical amino acids, metal binding protein
• 由来する生物種: Methanothermobacter thermautotrophicus
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 88871.12

構造登録者

Lee, Y.J.,Song, W.J. (登録日: 2025-06-04, 公開日: 2025-10-15, 最終更新日: 2026-01-21)

主引用文献

Lee, Y.,Moon, J.,Son, K.J.,Lee, J.,Ha, S.,Song, W.J.
Retrosynthetic Design of Dinuclear Copper Enzymes for Azide-Alkyne Cycloaddition via Clickable Noncanonical Amino Acids.
J.Am.Chem.Soc., 147:39408-39418, 2025

PubMed Abstract: Copper-catalyzed azide-alkyne cycloaddition (CuAAC) has enabled numerous synthetic and biological applications, driven by advances in the synthesis and optimization of copper-binding ligands. However, to the best of our knowledge, no bottom-up protein-based ligands have been specifically developed to catalyze this reaction. Here, we present a retrosynthetic protein design that leverages the introduction, duplication, and diversification of metal-chelating amino acid residues via a clickable noncanonical amino acid and CuAAC-mediated post-translational modification. A naturally occurring homodimer, dTDP-4-keto-6-deoxy-D-hexulose 3,5-epimerase, was engineered to structurally mimic the molecular framework of well-known CuAAC ligands, featuring multidentate triazole-containing motifs with four nitrogen donor atoms capable of accommodating two copper-binding sites. Remarkably, one protein construct R79TP exhibits CuAAC activity toward exogenous alkyne and azide substrates at rates exceeding that of a benchmark ligand, likely via a dinuclear mechanism. This work highlights the potential of genetically encoded precursors for multidentate ligand in proteins, expands the molecular complexity achievable in metalloenzyme engineering, and provides mechanistic insights and potential for copper-mediated bioorthogonal catalysis.

PubMed: 41117501
DOI: 10.1021/jacs.5c11725

実験手法

X-RAY DIFFRACTION (2.862 Å)