6VI5

Observing a ring-cleaving dioxygenase in action through a crystalline lens - a resting state structure

Summary for 6VI5

• Entry DOI: 10.2210/pdb6vi5/pdb
• Descriptor: 3-hydroxyanthranilate 3,4-dioxygenase, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, FE (II) ION, ... (5 entities in total)
• Functional Keywords: in crystallo reaction, extradiol dioxygenase, nad+ biosynthesis, intermediate, oxidoreductase
• Biological source: Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)
• Total number of polymer chains: 1
• Total formula weight: 22859.66

Authors

Wang, Y.,Liu, F.,Yang, Y.,Liu, A. (deposition date: 2020-01-12, release date: 2020-07-29, Last modification date: 2023-10-11)

Primary citation

Wang, Y.,Liu, K.F.,Yang, Y.,Davis, I.,Liu, A.
Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens.
Proc.Natl.Acad.Sci.USA, 117:19720-19730, 2020

PubMed Abstract: The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.

PubMed: 32732435
DOI: 10.1073/pnas.2005327117

Experimental method

X-RAY DIFFRACTION (1.604 Å)