Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane-associated N-terminal domain.
The flavin enzyme dihydroorotate dehydrogenase (DHOD; EC 1.3.99.11) catalyzes the oxidation of dihydroorotate to orotate, the fourth step in the de novo pyrimidine biosynthesis of UMP. The enzyme is a promising target for drug design in different biological and clinical applications for cancer and arthritis. The first crystal structure of the class 2 dihydroorotate dehydrogenase from rat has been determined in complex with its two inhibitors brequinar and atovaquone. These inhibitors have shown promising results as anti-proliferative, immunosuppressive, and antiparasitic agents. A unique feature of the class 2 DHODs is their N-terminal extension, which folds into a separate domain comprising two alpha-helices. This domain serves as the binding site for the two inhibitors and the respiratory quinones acting as the second substrate for the class 2 DHODs. The orientation of the first N-terminal helix is very different in the two complexes of rat DHOD (DHODR). Binding of atovaquone causes a 12 A movement of the first residue in the first alpha-helix. Based on the information from the two structures of DHODR, a model for binding of the quinone and the residues important for the interactions could be defined. His 56 and Arg 136, which are fully conserved in all class 2 DHODs, seem to play a key role in the interaction with the electron acceptor. The differences between the membrane-bound rat DHOD and membrane-associated class 2 DHODs exemplified by the Escherichia coli DHOD has been investigated by GRID computations of the hydrophobic probes predicted to interact with the membrane.
Hansen
Majbritt
M
Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.
Le Nours
Jérôme
J
Johansson
Eva
E
Antal
Torben
T
Ullrich
Alexandra
A
Löffler
Monika
M
Larsen
Sine
S
D000595:Amino Acid Sequence; D000814:Aniline Compounds / Q000737:chemistry / Q000378:metabolism*; D000818:Animals; D053626:Atovaquone; D001713:Biphenyl Compounds / Q000737:chemistry / Q000378:metabolism*; D002384:Catalysis; D003437:Crotonates; D018360:Crystallography, X-Ray; D000090722:Dihydroorotate Dehydrogenase; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D006885:Hydroxybutyrates / Q000737:chemistry / Q000378:metabolism*; D007166:Immunosuppressive Agents / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009285:Naphthoquinones / Q000737:chemistry / Q000378:metabolism*; D009570:Nitriles; D009963:Orotic Acid / Q000031:analogs & derivatives* / Q000737:chemistry; D044925:Oxidoreductases Acting on CH-CH Group Donors / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D051381:Rats; D016415:Sequence Alignment; D013379:Substrate Specificity; D014052:Toluidines; D011798:Quinaldines
D000814:Aniline Compounds; D053626:Atovaquone; D001713:Biphenyl Compounds; D003437:Crotonates; D000090722:Dihydroorotate Dehydrogenase; D004791:Enzyme Inhibitors; D006885:Hydroxybutyrates; D007166:Immunosuppressive Agents; D009285:Naphthoquinones; D009570:Nitriles; D009963:Orotic Acid; D044925:Oxidoreductases Acting on CH-CH Group Donors; D014052:Toluidines; C004768:4,5-dihydroorotic acid; C527525:teriflunomide; C046943:brequinar; D011798:Quinaldines