5NKN

Crystal structure of an Anticalin-colchicine complex

5NKN の概要

• エントリーDOI: 10.2210/pdb5nkn/pdb
• 分子名称: Neutrophil gelatinase-associated lipocalin, N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide (3 entities in total)
• 機能のキーワード: beta-barrel, colchicine, lcn2, lipocalin, ngal, protein engineering, transport protein
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 20342.14

構造登録者

Skerra, A.,Eichinger, A.,Barkovskiy, M. (登録日: 2017-03-31, 公開日: 2018-04-04, 最終更新日: 2024-10-23)

主引用文献

Barkovskiy, M.,Ilyukhina, E.,Dauner, M.,Eichinger, A.,Skerra, A.
An engineered lipocalin that tightly complexes the plant poison colchicine for use as antidote and in bioanalytical applications.
Biol. Chem., 400:351-366, 2019

PubMed Abstract: Colchicine is a toxic alkaloid prevalent in autumn crocus (Colchicum autumnale) that binds to tubulin and inhibits polymerization of microtubules. Using combinatorial and rational protein design, we have developed an artificial binding protein based on the human lipocalin 2 that binds colchicine with a dissociation constant of 120 pm, i.e. 10000-fold stronger than tubulin. Crystallographic analysis of the engineered lipocalin, dubbed Colchicalin, revealed major structural changes in the flexible loop region that forms the ligand pocket at the open end of the eight-stranded β-barrel, resulting in a lid-like structure over the deeply buried colchicine. A cis-peptide bond between residues Phe71 and Pro72 in loop #2 constitutes a peculiar feature and allows intimate contact with the tricyclic ligand. Using directed evolution, we achieved an extraordinary dissociation half-life of more than 9 h for the Colchicalin-colchicine complex. Together with the chemical robustness of colchicine and availability of activated derivatives, this also opens applications as a general-purpose affinity reagent, including facile quantification of colchicine in biological samples. Given that engineered lipocalins, also known as Anticalin® proteins, represent a class of clinically validated biopharmaceuticals, Colchicalin may offer a therapeutic antidote to scavenge colchicine and reverse its poisoning effect in situations of acute intoxication.

PubMed: 30517073
DOI: 10.1515/hsz-2018-0342

実験手法

X-RAY DIFFRACTION (2.2 Å)