7FDY

Structure of OmpF1

Summary for 7FDY

• Entry DOI: 10.2210/pdb7fdy/pdb
• Descriptor: Porin OmpF, ZINC ION (3 entities in total)
• Functional Keywords: membrane protein
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 111743.20

Authors

Jeong, W.J.,Song, W.J. (deposition date: 2021-07-18, release date: 2022-11-16, Last modification date: 2023-11-29)

Primary citation

Jeong, W.J.,Song, W.J.
Design and directed evolution of noncanonical beta-stereoselective metalloglycosidases.
Nat Commun, 13:6844-6844, 2022

PubMed Abstract: Metallohydrolases are ubiquitous in nearly all subclasses of hydrolases, utilizing metal elements to activate a water molecule and facilitate its subsequent dissociation of diverse chemical bonds. However, such a catalytic role of metal ions is rarely found with glycosidases that hydrolyze the glycosidic bonds in sugars. Herein, we design metalloglycosidases by constructing a hydrolytically active Zn-binding site within a barrel-shaped outer membrane protein OmpF. Structure- and mechanism-based redesign and directed evolution have led to the emergence of Zn-dependent glycosidases with catalytic proficiency of 2.8 × 10 and high β-stereoselectivity. Biochemical characterizations suggest that the Zn-binding site constitutes a key catalytic motif along with at least one adjacent acidic residue. This work demonstrates that unprecedented metalloenzymes can be tailor-made, expanding the scope of inorganic reactivities in proteinaceous environments, resetting the structural and functional diversity of metalloenzymes, and providing the potential molecular basis of unidentified metallohydrolases and novel whole-cell biocatalysts.

PubMed: 36369431
DOI: 10.1038/s41467-022-34713-8

Experimental method

X-RAY DIFFRACTION (3.1 Å)