Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes.

  title={Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes.},
  author={James H. Hurley and Antony M Dean and Daniel E. Koshland and Robert M. Stroud},
  volume={30 35},
The structures of NADP+ and magnesium isocitrate bound to the NADP(+)-dependent isocitrate dehydrogenase of Escherichia coli have been determined and refined at 2.5-A resolution. NADP+ is bound by the large domain of isocitrate dehydrogenase, a structure that has little similarity to the supersecondary structure of the nucleotide-binding domain of the lactate dehydrogenase-like family of nucleotide-binding proteins. The coenzyme-binding site confirms the fundamentally different evolution of the… 

Structure of isocitrate dehydrogenase with isocitrate, nicotinamide adenine dinucleotide phosphate, and calcium at 2.5-A resolution: a pseudo-Michaelis ternary complex.

The structure of isocitrate dehydrogenase (IDH) with a bound complex of isOCitrate, NADP+, and Ca2+ was solved at 2.5-A resolution and compared by difference mapping against previously determined enzymatic complexes to demonstrate stereospecificity of the enzyme-catalyzed reaction.

Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate.

These rearrangements are similar to the ligand-binding-induced movements observed in globins and insulin and serve as a model for an enzymatic mechanism which involves local shifts of secondary structural elements during turnover, rather than large-scale domain closures or loop transitions induced by substrate binding such as those observed in hexokinase or triosephosphate isomerase.

Oxidative inactivation of reduced NADP-generating enzymes in E. coli: iron-dependent inactivation with affinity cleavage of NADP-isocitrate dehydrogenase

Oxidative inactivation of NADP-isocitrate dehydration without affecting glucose 6-phosphate dehydrogenase shows only a little influence on the antioxidant activity supplying NADPH for glutathione regeneration, but may facilitate flux through the glyoxylate bypass as the biosynthetic pathway with the inhibition of the citric acid cycle under aerobic growth conditions of E. coli.

Kinetic analysis of NAD(+)-isocitrate dehydrogenase with altered isocitrate binding sites: contribution of IDH1 and IDH2 subunits to regulation and catalysis.

A model is presented which proposes that IDH1 functions as a regulatory subunit while IDH2 functions in catalysis, suggesting that the major subunit interactions within the octamer are between IDH 1 and IDH 2.

Crystal Structure of the Monomeric Isocitrate Dehydrogenase in the Presence of NADP+

Several structural features demonstrate that the monomeric IDHs are structurally more related to the eukaryotic dimeric IDhs than to the bacterial dimericIDHs.

Identification of Mn2+-binding Aspartates from α, β, and γ Subunits of Human NAD-dependent Isocitrate Dehydrogenase*

It is demonstrated that α-Asp-230 and α-asp-234 are critical for catalytic activity, but α- asparagine or cysteine is not needed; α- Asp- 230 and γ-AsP-215 may interact directly with the enzyme-bound Mn2+; and β- aspartates contribute to the affinity of the enzyme for NAD.

Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations

This study constitutes the first theoretical attempt to describe the entire catalytic cycle of hICDH, an enzyme involved in the regulation of tumorogenesis, and supports that the β-decarboxylation of oxalosuccinate is the most likely rate-limiting step.



Ionization of isocitrate bound to pig heart NADP+-dependent isocitrate dehydrogenase: 13C NMR study of substrate binding.

The 13C NMR spectrum of alpha-ketoglutarate remains unchanged in the presence of isocitrate dehydrogenase, implying the absence of alterations in geometry in the enzyme-bound form.

Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase.

It is suggested that the active site lies in an interdomain pocket close to the phosphorylation site of isocitrate dehydrogenase, which contains an unusual clasp-like domain in which both polypeptide chains in the dimer interlock are found.

Multinuclear NMR studies of the divalent metal binding site of NADP-dependent isocitrate dehydrogenase from pig heart.

The metal activator site of NADP-dependent isocitrate dehydrogenase from pig heart has been probed by using 113Cd and 25Mg NMR as well as manganese paramagnetic relaxation of nuclei in the fast-exchanging ligands alpha-ketoglutarate and adenosine 2'-monophosphate to locate the divalent metal within the active site.

[The enzymatic properties of isocitric dehydrogenase].

1H nuclear magnetic resonance studies of the conformation and environment of nucleotides bound to pig heart NADP+-dependent isocitrate dehydrogenase.

The binding of coenzymes, NADP+ and NADPH, and coenzyme fragments, 2'-phosphoadenosine 5'-(diphosphoribose), adenosine 2',5'-bisphosphate, and 2'-AMP, to pig heart NADP+-dependent isocitrate

Structure of the medium-chain acyl-CoA dehydrogenase from pig liver mitochondria at 3-A resolution.

  • J. J. KimJ. Wu
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1988
The three-dimensional structure of the medium-chain acyl-CoA dehydrogenase (EC from pig liver mitochondria has been determined to 3.0-A resolution by the x-ray diffraction method. The

Site-directed mutagenesis reveals role of mobile arginine residue in lactate dehydrogenase catalysis

Transient kinetic and equilibrium studies of the mutant enzyme indicate that arginine 109 enhances the polarization of the pyruvate carbonyl group in the ground state and stabilizes the transition state.

Isotope effect studies of the chemical mechanism of pig heart NADP isocitrate dehydrogenase.

The catalytic mechanism of porcine heart NADP isocitrate dehydrogenase has been investigated by use of the variation of deuterium and 13C kinetic isotope effects with pH and the forward commitment to catalysis for decarboxylation was determined to be 7.5%.