9PAS

Crystal structure of Rv0097 G204F variant with vanadyl and CADA bound

9PAS の概要

• エントリーDOI: 10.2210/pdb9pas/pdb
• 分子名称: (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase, ACETATE ION, oxovanadium(2+), ... (5 entities in total)
• 機能のキーワード: non-heme iron enzyme, fe(ii)/alpha-ketoglutarate-dependent dioxygenases, isonitrile synthase, oxidoreductase
• 由来する生物種: Mycobacterium tuberculosis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 69160.54

構造登録者

Ye, N.,Drennan, C.L. (登録日: 2025-06-25, 公開日: 2026-03-11)

主引用文献

Ye, N.,Del Rio Flores, A.,Zhang, W.,Drennan, C.L.
A highly dynamic mononuclear non-heme iron enzyme for the two-step isonitrile biosynthesis.
Nat Commun, 17:-, 2026

PubMed Abstract: The recent discovery of the isonitrile biosynthetic enzyme ScoE expanded the catalytic repertoire of the Fe(II)/αKG-dependent dioxygenase enzyme family. ScoE synthesizes an isonitrile functional group from a glycyl-fatty acid adduct, with both the isonitrile nitrogen and carbon atoms coming from the glycyl moiety. This challenging chemistry cannot be performed in a single step. Instead, the mechanism appears to require two half reactions, each involving αKG cleavage to generate a highly reactive iron-oxygen species. Here, we report sixteen crystal structures that provide snapshots along the reaction trajectory of Rv0097, a ScoE homolog from Mycobacterium tuberculosis. These structures, which are both of wild-type and Rv0097 variants, include a substrate 3-((carboxymethyl)amino)decanoic acid (CADA)-bound structure, an αKG-bound structure, and a structure with both CADA and αKG bound. These structural data reveal how Rv0097 employs conformational rearrangements to protect the unstable CADA-reaction intermediate that is formed in the first half reaction while swapping out αKG cleavage products for a second molecule of αKG. Additionally, these structures, together with data from site-directed mutagenesis, provide insight into Rv0097's preference for substrates with long alkyl chains, potentially facilitating efforts to re-engineer ScoE/Rv0097 to synthesize isonitrile functional groups on a wider range of small molecules.

PubMed: 41587996
DOI: 10.1038/s41467-026-68588-w

実験手法

X-RAY DIFFRACTION (1.55 Å)