5FLI

enzyme-substrate complex of Ni-quercetinase

Summary for 5FLI

• Entry DOI: 10.2210/pdb5fli/pdb
• Related: 5FLE 5FLH 5FLJ
• Descriptor: QUERCETINASE QUED, NICKEL (II) ION, 3,5,7,3',4'-PENTAHYDROXYFLAVONE, ... (4 entities in total)
• Functional Keywords: oxidoreductase, dioxygenase, nickel, quercetin, streptomyces, ni-quuercetinase
• Biological source: STREPTOMYCES SP. FLA
• Total number of polymer chains: 12
• Total formula weight: 257151.66

Authors

Jeoung, J.-H.,Nianios, D.,Fetzner, S.,Dobbek, H. (deposition date: 2015-10-26, release date: 2016-06-01, Last modification date: 2024-01-10)

Primary citation

Jeoung, J.H.,Nianios, D.,Fetzner, S.,Dobbek, H.
Quercetin 2,4-Dioxygenase Activates Dioxygen in a Side-On O2-Ni Complex.
Angew. Chem. Int. Ed. Engl., 55:3281-3284, 2016

PubMed Abstract: Quercetin 2,4-dioxygenase (quercetinase) from Streptomyces uses nickel as the active-site cofactor to catalyze oxidative cleavage of the flavonol quercetin. How this unusual active-site metal supports catalysis and O2 activation is under debate. We present crystal structures of Ni-quercetinase in three different states, thus providing direct insight into how quercetin and O2 are activated at the Ni(2+) ion. The Ni(2+) ion is coordinated by three histidine residues and a glutamate residue (E(76)) in all three states. Upon binding, quercetin replaces one water ligand at Ni and is stabilized by a short hydrogen bond through E(76) , the carboxylate group of which rotates by 90°. This conformational change weakens the interaction between Ni and the remaining water ligand, thereby preparing a coordination site at Ni to bind O2. O2 binds side-on to the Ni(2+) ion and is perpendicular to the C2-C3 and C3-C4 bonds of quercetin, which are cleaved in the following reaction steps.

PubMed: 26846734
DOI: 10.1002/anie.201510741

Experimental method

X-RAY DIFFRACTION (2.15 Å)