PMID: 28098230

Authors:

Ma T, Peng Y, Huang W, Ding J

Title:

Molecular mechanism of the allosteric regulation of the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.

Journal:

Sci Rep. 2017 Jan 18;7:40921. doi: 10.1038/srep40921.

Abstract:

Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate in the Krebs cycle. It exists as the alpha2betagamma heterotetramer composed of the alphabeta and alphagamma heterodimers. Previously, we have demonstrated biochemically that the alpha2betagamma heterotetramer and alphagamma heterodimer can be allosterically activated by citrate (CIT) and ADP. In this work, we report the crystal structures of the alphagamma heterodimer with the gamma subunit bound without or with different activators. Structural analyses show that CIT, ADP and Mg2+ bind adjacent to each other at the allosteric site. The CIT binding induces conformational changes at the allosteric site, which are transmitted to the active site through the heterodimer interface, leading to stabilization of the ICT binding at the active site and thus activation of the enzyme. The ADP binding induces no further conformational changes but enhances the CIT binding through Mg2+-mediated interactions, yielding a synergistic activation effect. ICT can also bind to the CIT-binding subsite, which induces similar conformational changes but exhibits a weaker activation effect. The functional roles of the key residues are verified by mutagenesis, kinetic and structural studies. Our structural and functional data together reveal the molecular mechanism of the allosteric regulation of the alphagamma heterodimer.