7FDY image
Deposition Date 2021-07-18
Release Date 2022-11-16
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7FDY
Title:
Structure of OmpF1
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.10 Å
R-Value Free:
0.29
R-Value Work:
0.26
R-Value Observed:
0.27
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Porin OmpF
Chain IDs:A, B, C
Chain Length:341
Number of Molecules:3
Biological Source:Escherichia coli
Ligand Molecules
Primary Citation
Design and directed evolution of noncanonical beta-stereoselective metalloglycosidases.
Nat Commun 13 6844 6844 (2022)
PMID: 36369431 DOI: 10.1038/s41467-022-34713-8

Abstact

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 × 109 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.

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