8HFB

Evolved variant of quercetin 2,4-dioxygenase from Bacillus subtilis

Summary for 8HFB

• Entry DOI: 10.2210/pdb8hfb/pdb
• Descriptor: Quercetin 2,3-dioxygenase, 1,2-ETHANEDIOL, GLYCEROL, ... (5 entities in total)
• Functional Keywords: quercetinase, oxidoreductase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 75718.08

Authors

Eom, H.,Song, W.J. (deposition date: 2022-11-10, release date: 2023-03-08, Last modification date: 2024-05-22)

Primary citation

Eom, H.,Cao, Y.,Kim, H.,de Visser, S.P.,Song, W.J.
Underlying Role of Hydrophobic Environments in Tuning Metal Elements for Efficient Enzyme Catalysis.
J.Am.Chem.Soc., 145:5880-5887, 2023

PubMed Abstract: The catalytic functions of metalloenzymes are often strongly correlated with metal elements in the active sites. However, dioxygen-activating nonheme quercetin dioxygenases (QueD) are found with various first-row transition-metal ions when metal swapping inactivates their innate catalytic activity. To unveil the molecular basis of this seemingly promiscuous yet metal-specific enzyme, we transformed manganese-dependent QueD into a nickel-dependent enzyme by sequence- and structure-based directed evolution. Although the net effect of acquired mutations was primarily to rearrange hydrophobic residues in the active site pocket, biochemical, kinetic, X-ray crystallographic, spectroscopic, and computational studies suggest that these modifications in the secondary coordination spheres can adjust the electronic structure of the enzyme-substrate complex to counteract the effects induced by the metal substitution. These results explicitly demonstrate that such noncovalent interactions encrypt metal specificity in a finely modulated manner, revealing the underestimated chemical power of the hydrophobic sequence network in enzyme catalysis.

PubMed: 36853654
DOI: 10.1021/jacs.2c13337

Experimental method

X-RAY DIFFRACTION (2.24 Å)