Dimerization interface of 3-hydroxyacyl-CoA dehydrogenase tunes the formation of its catalytic intermediate.
3-Hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35) is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD) that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A) with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60-80) that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
Yingzhi
Y
Xu
Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, Jilin University, Changchun, China.
He
H
Li
Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, Jilin University, Changchun, China.
Ying-Hua
YH
Jin
Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, China.
Jun
J
Fan
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Fei
F
Sun
D015094:3-Hydroxyacyl CoA Dehydrogenases / Q000737:chemistry* / Q000235:genetics; D000818:Animals; D055162:Biocatalysis; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry* / Q000235:genetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D055503:Protein Multimerization
D029742:Caenorhabditis elegans Proteins; D015094:3-Hydroxyacyl CoA Dehydrogenases