7CA0

Crystal structure of dihydroorotase in complex with 5-fluoroorotic acid from Saccharomyces cerevisiae

Summary for 7CA0

• Entry DOI: 10.2210/pdb7ca0/pdb
• Related: 6L0A 6L0B
• Descriptor: Dihydroorotase, ZINC ION, 5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID, ... (4 entities in total)
• Functional Keywords: dihydropyrimidinase dihydroorotase metalloenzyme, hydrolase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Total number of polymer chains: 4
• Total formula weight: 167133.04

Authors

Guan, H.H.,Huang, Y.H.,Huang, C.Y.,Chen, C.J. (deposition date: 2020-06-08, release date: 2021-06-09, Last modification date: 2023-11-29)

Primary citation

Guan, H.H.,Huang, Y.H.,Lin, E.S.,Chen, C.J.,Huang, C.Y.
Complexed Crystal Structure of Saccharomyces cerevisiae Dihydroorotase with Inhibitor 5-Fluoroorotate Reveals a New Binding Mode.
Bioinorg Chem Appl, 2021:2572844-2572844, 2021

PubMed Abstract: Dihydroorotase (DHOase) possesses a binuclear metal center in which two Zn ions are bridged by a posttranslationally carbamylated lysine. DHOase catalyzes the reversible cyclization of -carbamoyl aspartate (CA-asp) to dihydroorotate (DHO) in the third step of the pathway for the biosynthesis of pyrimidine nucleotides and is an attractive target for potential anticancer and antimalarial chemotherapy. Crystal structures of ligand-bound DHOase show that the flexible loop extends toward the active site when CA-asp is bound (loop-in mode) or moves away from the active site, facilitating the product DHO release (loop-out mode). DHOase binds the product-like inhibitor 5-fluoroorotate (5-FOA) in a similar mode to DHO. In the present study, we report the crystal structure of DHOase from (ScDHOase) complexed with 5-FOA at 2.5 Å resolution (PDB entry 7CA0). ScDHOase shares structural similarity with DHOase (EcDHOase). However, our complexed structure revealed that ScDHOase bound 5-FOA differently from EcDHOase. 5-FOA ligated the Zn atoms in the active site of ScDHOase. In addition, 5-FOA bound to ScDHOase through the loop-in mode. We also characterized the binding of 5-FOA to ScDHOase by using the site-directed mutagenesis and fluorescence quenching method. Based on these lines of molecular evidence, we discussed whether these different binding modes are species- or crystallography-dependent.

PubMed: 34630544
DOI: 10.1155/2021/2572844

Experimental method

X-RAY DIFFRACTION (2.5 Å)