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

Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the α(2)βγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demonstrated biochemically that the α(2)βγ heterotetramer and αγ...

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Autores principales: Ma, Tengfei, Peng, Yingjie, Huang, Wei, Ding, Jianping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241874/
https://www.ncbi.nlm.nih.gov/pubmed/28098230
http://dx.doi.org/10.1038/srep40921
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author Ma, Tengfei
Peng, Yingjie
Huang, Wei
Ding, Jianping
author_facet Ma, Tengfei
Peng, Yingjie
Huang, Wei
Ding, Jianping
author_sort Ma, Tengfei
collection PubMed
description Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the α(2)βγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demonstrated biochemically that the α(2)βγ 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(2+) 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(2+)-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.
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spelling pubmed-52418742017-01-23 Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase Ma, Tengfei Peng, Yingjie Huang, Wei Ding, Jianping Sci Rep Article Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the α(2)βγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demonstrated biochemically that the α(2)βγ 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(2+) 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(2+)-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. Nature Publishing Group 2017-01-18 /pmc/articles/PMC5241874/ /pubmed/28098230 http://dx.doi.org/10.1038/srep40921 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Ma, Tengfei
Peng, Yingjie
Huang, Wei
Ding, Jianping
Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase
title Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase
title_full Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase
title_fullStr Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase
title_full_unstemmed Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase
title_short Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase
title_sort molecular mechanism of the allosteric regulation of the αγ heterodimer of human nad-dependent isocitrate dehydrogenase
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5241874/
https://www.ncbi.nlm.nih.gov/pubmed/28098230
http://dx.doi.org/10.1038/srep40921
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