Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins.
BACKGROUND
Old yellow enzyme (OYE) was the first flavoenzyme purified, but its function is still unknown. Nevertheless, the NADPH oxidase activity, the flavin mononucleotide environment and the ligand-binding properties of OYE have been extensively studied by biochemical and spectroscopic approaches. Full interpretation of these data requires structural information.


RESULTS
The crystal structures of oxidized and reduced OYE at 2 A resolution reveal an alpha/beta-barrel topology clearly related to trimethylamine dehydrogenase. Complexes of OYE with p-hydroxybenzaldehyde, beta-estradiol, and an NADPH analog show all three binding at a common site, stacked on the flavin. The putative NADPH binding mode is novel as it involves primary recognition of the nicotinamide mononucleotide portion.


CONCLUSIONS
This work shows that the striking spectral changes seen upon phenol binding are due to close physical association of the flavin and phenolate. It also identifies the structural class of OYE and suggests that if NADPH is its true substrate, then OYE has adopted NADPH dependence during evolution.
Fox
K M
KM
Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853.
Karplus
P A
PA
D000595:Amino Acid Sequence; D001547:Benzaldehydes / Q000737:chemistry; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004563:Electrochemistry; D004958:Estradiol / Q000737:chemistry; D005486:Flavin Mononucleotide / Q000737:chemistry; D005420:Flavoproteins / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009249:NADP / Q000737:chemistry; D009252:NADPH Dehydrogenase / Q000737:chemistry* / Q000235:genetics; D010084:Oxidation-Reduction; D011487:Protein Conformation; D012440:Saccharomyces / Q000201:enzymology / Q000235:genetics; D017386:Sequence Homology, Amino Acid
D001547:Benzaldehydes; D005420:Flavoproteins; D008024:Ligands; D004958:Estradiol; D009249:NADP; D005486:Flavin Mononucleotide; D009252:NADPH Dehydrogenase; C011483:4-hydroxybenzaldehyde