7QPO

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

Summary for 7QPO

• Entry DOI: 10.2210/pdb7qpo/pdb
• Descriptor: Trans-3-hydroxy-L-proline dehydratase (2 entities in total)
• Functional Keywords: hydroxyproline, dehydratase, lyase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 81200.49

Authors

Ferrario, E.,Miggiano, R.,Rizzi, M.,Ferraris, D.M. (deposition date: 2022-01-05, release date: 2022-08-17, Last modification date: 2024-10-23)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (3 Å)