5FLJ

enzyme-substrate-dioxygen complex of Ni-quercetinase

Summary for 5FLJ

• Entry DOI: 10.2210/pdb5flj/pdb
• Related: 5FLE 5FLH 5FLI
• Descriptor: QUERCETINASE QUED, NICKEL (II) ION, 3,5,7,3',4'-PENTAHYDROXYFLAVONE, ... (6 entities in total)
• Functional Keywords: oxidoreductase, dioxygenase, nickel, streptomyces, ni-quercetinase, dioxygen
• Biological source: STREPTOMYCES SP.
• Total number of polymer chains: 12
• Total formula weight: 258689.88

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.,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-, 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 (1.818 Å)