6VXE

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound

6VXE の概要

• エントリーDOI: 10.2210/pdb6vxe/pdb
• 分子名称: Trans-4-hydroxy-L-proline dehydratase, 4-HYDROXYPROLINE (3 entities in total)
• 機能のキーワード: glycyl radical enzyme, hydroxyproline dehydratase, lyase
• 由来する生物種: Clostridioides difficile 70-100-2010
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 732701.91

構造登録者

Backman, L.R.F.,Drennan, C.L. (登録日: 2020-02-21, 公開日: 2020-04-08, 最終更新日: 2023-10-11)

主引用文献

Backman, L.R.,Huang, Y.Y.,Andorfer, M.C.,Gold, B.,Raines, R.T.,Balskus, E.P.,Drennan, C.L.
Molecular basis for catabolism of the abundant metabolitetrans-4-hydroxy-L-proline by a microbial glycyl radical enzyme.
Elife, 9:-, 2020

PubMed Abstract: The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, -4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to ()-Δ-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.

PubMed: 32180548
DOI: 10.7554/eLife.51420

実験手法

X-RAY DIFFRACTION (2.464 Å)