5GRE

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+), citrate and ADP

Summary for 5GRE

• Entry DOI: 10.2210/pdb5gre/pdb
• Related: 5GRF 5GRH 5GRI 5GRL
• Descriptor: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial, Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: cit, adp, allosteric regulation, oxidoreductase
• Biological source: Homo sapiens (Human); More
• Cellular location: Mitochondrion: P50213 P51553
• Total number of polymer chains: 2
• Total formula weight: 76217.63

Authors

Ma, T.,Peng, Y.,Ding, J. (deposition date: 2016-08-11, release date: 2017-02-15, Last modification date: 2023-11-08)

Primary citation

Ma, T.,Peng, Y.,Huang, W.,Ding, J.
Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
Sci Rep, 7:40921-40921, 2017

PubMed Abstract: Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the αβγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demonstrated biochemically that the αβγ heterotetramer and αγ heterodimer can be allosterically activated by citrate (CIT) and ADP. In this work, we report the crystal structures of the αγ heterodimer with the γ subunit bound without or with different activators. Structural analyses show that CIT, ADP and Mg 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 Mg-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 αγ heterodimer.

PubMed: 28098230
DOI: 10.1038/srep40921

Experimental method

X-RAY DIFFRACTION (2.65 Å)