2W55: Crystal Structure Of Xanthine Dehydrogenase (e232q Variant) From Rhodobacter Capsulatus In Complex With Hypoxanthine

Citation:
Abstract
Rhodobacter capsulatus xanthine dehydrogenase (XDH) is an (alphabeta)(2) heterotetrameric cytoplasmic enzyme that resembles eukaryotic xanthine oxidoreductases in respect to both amino acid sequence and structural fold. To obtain a detailed understanding of the mechanism of substrate and inhibitor binding at the active site, we solved crystal structures of R. capsulatus XDH in the presence of its substrates hypoxanthine, xanthine, and the inhibitor pterin-6-aldehyde using either the inactive desulfo form of the enzyme or an active site mutant (E(B)232Q) to prevent substrate turnover. The hypoxanthine- and xanthine-bound structures reveal the orientation of both substrates at the active site and show the importance of residue Glu(B)-232 for substrate positioning. The oxygen atom at the C-6 position of both substrates is oriented toward Arg(B)-310 in the active site. Thus the substrates bind in an orientation opposite to the one seen in the structure of the reduced enzyme with the inhibitor oxypurinol. The tightness of the substrates in the active site suggests that the intermediate products must exit the binding pocket to allow first the attack of the C-2, followed by oxidation of the C-8 atom to form the final product uric acid. Structural studies of pterin-6-aldehyde, a potent inhibitor of R. capsulatus XDH, contribute further to the understanding of the relative positioning of inhibitors and substrates in the binding pocket. Steady state kinetics reveal a competitive inhibition pattern with a K(i) of 103.57 +/- 18.96 nm for pterin-6-aldehyde.
PDB ID: 2W55Download
MMDB ID: 68608
PDB Deposition Date: 2008/12/4
Updated in MMDB: 2008/12
Experimental Method:
x-ray diffraction
Resolution: 3.4  Å
Source Organism:
Similar Structures:
Biological Unit for 2W55: dimeric; determined by author and by software (PQS)
Molecular Components in 2W55
Label Count Molecule
Proteins (2 molecules)
1
Xanthine Dehydrogenase
Molecule annotation
1
Xanthine Dehydrogenase
Molecule annotation
Chemicals (7 molecules)
1
3
2
1
3
1
4
1
5
1
* Click molecule labels to explore molecular sequence information.

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