8GKP

Crystal Structure Analysis of Aspergillus fumigatus alkaline protease

Summary for 8GKP

• Entry DOI: 10.2210/pdb8gkp/pdb
• Descriptor: Alkaline protease 1, FORMIC ACID, PHENYLMETHYLSULFONYL FLUORIDE, ... (8 entities in total)
• Functional Keywords: alpha-beta hydrolase, hydrolase
• Biological source: Aspergillus fumigatus Af293; More
• Total number of polymer chains: 4
• Total formula weight: 80181.13

Authors

Fernandez, D.,Diec, D.D.L.,Guo, W.,Russi, S. (deposition date: 2023-03-20, release date: 2023-11-01, Last modification date: 2024-10-30)

Primary citation

Pattelli, O.N.,Diec, D.D.L.,Guo, W.,Russi, S.,Fernandez, D.
Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision.
Sci Rep, 13:17926-17926, 2023

PubMed Abstract: We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His-Asp-Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1'-S4' substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1-S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

PubMed: 37864071
DOI: 10.1038/s41598-023-45028-z

Experimental method

X-RAY DIFFRACTION (1.55 Å)