1V97

Crystal Structure of Bovine Milk Xanthine Dehydrogenase FYX-051 bound form

Summary for 1V97

• Entry DOI: 10.2210/pdb1v97/pdb
• Descriptor: Xanthine dehydrogenase, CALCIUM ION, FE2/S2 (INORGANIC) CLUSTER, ... (10 entities in total)
• Functional Keywords: xanthine dehydrogenase, molybdopterin, fyx-051, reaction intermediate, oxidoreductase
• Biological source: Bos taurus (cattle)
• Cellular location: Cytoplasm (By similarity): P80457
• Total number of polymer chains: 2
• Total formula weight: 298806.89

Authors

Okamoto, K.,Matsumoto, K.,Hille, R.,Eger, B.T.,Pai, E.F.,Nishino, T. (deposition date: 2004-01-21, release date: 2004-06-22, Last modification date: 2023-12-27)

Primary citation

Okamoto, K.,Matsumoto, K.,Hille, R.,Eger, B.T.,Pai, E.F.,Nishino, T.
The crystal structure of xanthine oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition.
Proc.Natl.Acad.Sci.USA, 101:7931-7936, 2004

PubMed Abstract: Molybdenum is widely distributed in biology and is usually found as a mononuclear metal center in the active sites of many enzymes catalyzing oxygen atom transfer. The molybdenum hydroxylases are distinct from other biological systems catalyzing hydroxylation reactions in that the oxygen atom incorporated into the product is derived from water rather than molecular oxygen. Here, we present the crystal structure of the key intermediate in the hydroxylation reaction of xanthine oxidoreductase with a slow substrate, in which the carbon-oxygen bond of the product is formed, yet the product remains complexed to the molybdenum. This intermediate displays a stable broad charge-transfer band at approximately 640 nm. The crystal structure of the complex indicates that the catalytically labile Mo-OH oxygen has formed a bond with a carbon atom of the substrate. In addition, the MoS group of the oxidized enzyme has become protonated to afford Mo-SH on reduction of the molybdenum center. In contrast to previous assignments, we find this last ligand at an equatorial position in the square-pyramidal metal coordination sphere, not the apical position. A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide.

PubMed: 15148401
DOI: 10.1073/pnas.0400973101

Experimental method

X-RAY DIFFRACTION (1.94 Å)