Ligand-assisted inhibition in cytochrome P450 158A2 from Streptomyces coelicolor A3(2).
Cytochrome P450 158A2 (CYP158A2) can polymerize flaviolin to red-brown pigments, which may afford physical protection to the organism, possibly against the deleterious effects of UV radiation. We have found that the small molecule malonic acid enables cocrystallization of this mixed function oxidase with the azole inhibitor 4-phenylimidazole. The presence of malonate molecules affects the behavior of the binding of 4-phenylimidazole to CYP158A2 and increases inhibition potency up to 2-fold compared to 4-phenylimidazole alone. We report here the crystal structure of the 4-phenylimidazole/malonate complex of CYP158A2 at 1.5 A. Two molecules of malonate used in crystallization are found above the single inhibitor molecule in the active site. Those two molecules are linked between the BC loop and beta 1-4/beta 6-1 strands via hydrogen bond interactions to stabilize the conformational changes of the BC loop and beta strands that take place upon inhibitor binding compared to the ligand-free structure we have reported previously. 4-Phenylimidazole can launch an extensive hydrogen-bonding network in the region of the F/G helices which may stabilize the conformational changes. Our findings clearly show that two molecules of malonate assist the inhibitor 4-phenylimidazole to assume a specific location producing more inhibition in the enzyme catalytic activity.
Zhao
Bin
B
Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA. bin.zhao@vanderbilt.edu
Waterman
Michael R
MR
Isin
Emre M
EM
Sundaramoorthy
Munirathinam
M
Podust
Larissa M
LM
D001665:Binding Sites; D003460:Crystallization; D065607:Cytochrome P-450 Enzyme Inhibitors; D004926:Escherichia coli / Q000235:genetics; D006860:Hydrogen Bonding; D007093:Imidazoles / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D008024:Ligands; D008314:Malonates / Q000737:chemistry / Q000378:metabolism; D006899:Mixed Function Oxygenases / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D009285:Naphthoquinones / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D048372:Streptomyces coelicolor / Q000201:enzymology*
D065607:Cytochrome P-450 Enzyme Inhibitors; D007093:Imidazoles; D008024:Ligands; D008314:Malonates; D009285:Naphthoquinones; C041659:flaviolin; C033023:4(5)-phenylimidazole; C030290:malonic acid; D006899:Mixed Function Oxygenases