7QPO

Crystal structure of human trans-3-Hydroxy-L-proline dehydratase

7QPO の概要

• エントリーDOI: 10.2210/pdb7qpo/pdb
• 分子名称: Trans-3-hydroxy-L-proline dehydratase (2 entities in total)
• 機能のキーワード: hydroxyproline, dehydratase, lyase
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 81200.49

構造登録者

Ferrario, E.,Miggiano, R.,Rizzi, M.,Ferraris, D.M. (登録日: 2022-01-05, 公開日: 2022-08-17, 最終更新日: 2024-10-23)

主引用文献

Ferrario, E.,Miggiano, R.,Rizzi, M.,Ferraris, D.M.
The integration of AlphaFold-predicted and crystal structures of human trans -3-hydroxy-l-proline dehydratase reveals a regulatory catalytic mechanism.
Comput Struct Biotechnol J, 20:3874-3883, 2022

PubMed Abstract: Computational methods for protein structure prediction have made significant strides forward, as evidenced by the last development of the neural network AlphaFold, which outperformed the CASP14 competitors by consistently predicting the structure of target proteins. Here we show an integrated structural investigation that combines the AlphaFold and crystal structures of human -3-Hydroxy-l-proline dehydratase, an enzyme involved in hydroxyproline catabolism and whose structure had never been reported before, identifying a structural element, absent in the AlphaFold model but present in the crystal structure, that was subsequently proved to be functionally relevant. Although the AlphaFold model lacked information on protein oligomerization, the native dimer was reconstructed using template-based and computational approaches. Moreover, molecular phasing of the diffraction data using the AlphaFold model resulted in dimer reconstruction and straightforward structure solution. Our work adds to the integration of AlphaFold with experimental structural and functional data for protein analysis, crystallographic phasing and structure solution.

PubMed: 35891782
DOI: 10.1016/j.csbj.2022.07.027

実験手法

X-RAY DIFFRACTION (3 Å)