Pyridine Nucleotide-Dependent b-Hydroxyacid Oxidative decarboxylases: An Overview. Pp. 281-286.
Structural Studies of A Human Malic Enzyme. Pp. 287-296.
NAD-Malic Enzyme from Ascaris suum: Sequence and Structural Studies. Pp. 297-304.
G.S. Jagannatha Rao, David E. Coleman, G. Kulkarni,
E.J. Goldsmith, Paul F. Cook and Ben G. Harris
Chemical Mechanism of Malic Enzyme as Determined by Isotope Effects and Alternate Substrates. Pp. 305-312.
W.W. Cleland
Chemical Mechanism of 6-Phosphogluconate Dehydrogenase via Kinetic Studies and Site-Directed Mutagenesis. Pp. 313-322.
Lei Zhang and
Paul F. Cook
Tartrate Dehydrogenase, an Enzyme With Multiple Catalytic Activities. Pp. 323-332.
Peter A.
Tipton
Structure and Thermostability of 3-Isopropylmalate Dehydrogenase. Pp. 333-340.
Nobuo Tanaka
and Tairo Oshima
6-Phosphogluconate Dehydrogenase: Structural Symmetry and Functional Asymmetry. Pp. 341-348.
Mario Rippa,
Stefania Hanau, Carlo Cervellati and Franco Dallocchio
[Back to top] Pyridine Nucleotide-Dependent b-Hydroxyacid Oxidative decarboxylases: An Overview.
William E. Karsten and Paul F.
Cook
The class of pyridine nucleotide-dependent b-hydroxyacid oxidative decarboxylases generally catalyze the oxidative decarboxylation of a b-hydroxyacid to a ketone and CO2 using NAD(P)+ as the oxidatt. There are two subclasses based on the metal-dependence of the reaction. Enzymes that have substrates with electron withdrawing substituents in the a-and or g-position generally do not require a metal ion cofactor, an example is 6-phosphogluconate dehydrogenase. Of the remaining enzymes, some require only a divalent metal ion, e.g. malic enzyme, while the others require both a monovalent and a divalent metal ion, for example tartate dehydrogenase.
[Back to top] Structural Studies of A Human Malic Enzyme.
Zhiru Yang, Liang Tong
Structural studies of the human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD-ME) establish that malic enzymes belong to a new class of oxidative decarboxylases. An open and a closed form of the enzyme have been observed from the crystallographic analysis, with the closed form also revealing the binding modes of the divalent cation and the transition-state analog inhibitor oxalate. The structures show that E255, D256 and D279 are the ligands of the cation, and suggest that Y112 and K183 may be the catalytic residues of the enzyme.
[Back to top] NAD-Malic Enzyme from Ascaris suum: Sequence and Structural Studies.
G.S.
Jagannatha Rao, David E. Coleman, G. Kulkarni, E.J. Goldsmith, Paul F. Cook and
Ben G. Harris
Ascaris suum malic enzyme belongs to the class of oxidative decarboxylases and converts L-Malate to pyruvate utilizing NAD and a divalent metal cofactor. It plays a key role in the energy metabolism of the parasite and hence is a target for chemotherapy. It has been extensively characterized from the standpoint of its kinetic, regulatory and chemical mechanisms. Recent studies involving site specific mutants and the determination of its complete sequence as well as quaternary structure have greatly facilitated elucidation of its catalytic mecanism.
[Back to top] Chemical Mechanism of Malic Enzyme as Determined by Isotope Effects and Alternate Substrates.
W.W. Cleland
Isotope effect studies have shown that malic enzyme from avian liver or Ascaris suum has a stepwise mechanism with NAD(P) as substrate, but a concerted one with nucleotide substrates with higher redox potentials. It has been possible to calculate intrinsic deuterium and 13C isotope effects and commitments. The enzyme is very specific, with only erythro-fluoromalate, D-and mesotartrate and L-aspartate with an unprotonated amino group as slow alternate substrates.
[Back to top] Chemical Mechanism of 6-Phosphogluconate Dehydrogenase via Kinetic Studies and Site-Directed Mutagenesis.
Lei Zhang and
Paul F. Cook
6-Phosphogluconate dehydrogenase catalyzes the metal ion-independent oxidative decarboxylation of 6-phosphogluconate (6PG). The enzyme catalyzes a reaction in which 6PG is first oxidized at the 3-position, then decarboxylated to the 1,2-enediol of Ru5P, and then tautomerized to give the Ru5P ketone product. In the reaction, K183 acts as a general base, general acid, shuttling a proton between the 3-hydroxyl and itself, and E190 acts as a general acid to protonate C1 of the enediol intermediate in the tautomerization step.
[Back to top] Tartrate Dehydrogenase, an Enzyme With Multiple Catalytic Activities.
Peter A.
Tipton
Tartrate dehydrogenase is found in a variety of microorganisms and operates as part of a pathway by which tartrate is converted into D-glycerate, providing entry for the carbon into primary metabolic pathways. Tartrate dehydrogenase was isolated from Pseudomonas putida grown on (+)-tartrate as the sole carbon source and characterized in the 1960’s [1]. More recently, TDH was isolated from the same bacterial strain and its gene was cloned [2]. The properties of that enzyme are similar in several respects to the TDH described in the earlier work, but differ in several key features as well . It is difficult to know whether the discrepancies arose because different enzymes were isolated and studied or whether mutations occurred which changed the functional properties of the enzyme. A number of workers have described enzymes which turn over tartrate [3,4], but this article will concentrate on the recently isolated P. putida TDH, which exhibited several fascinating mechanistic features.
[Back to top] Structure and Thermostability of 3-Isopropylmalate Dehydrogenase.
Nobuo Tanaka
and Tairo Oshima
The thermostability of 3-isopropylmlate dehydrogenase (IPMDH) is reviewed based on its three dimensional structure. The three dimensional structures of an extreme thermophilic, mesophilic and chimeric enzymes are found to be similar with one another, although they have the same function and different thermostabilities. They are composed of two identical monomers, each of which is comprised of two domains. The open and closed conformation, in each subunit, has been determined from the three-dimensional structures , and site-directed mutagenesis, residues have been identified that contribute to the thermal stability of the IPMDH.
[Back to top] 6-Phosphogluconate Dehydrogenase: Structural Symmetry and Functional Asymmetry.
Mario Rippa,
Stefania Hanau, Carlo Cervellati and Franco Dallocchio
6-Phosphogluconate dehydrogenase catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate through an oxidation, a decarboxylation and a tautomerization. The two subunits in the crystals of the dimeric sheep liver enzyme have the same conformation, as te apoenzyme and with the substrate or coenzyme. An hypothesis is now advanced that in solution, during catalysis, the two subunits have a different alternating role and thus a functional asymmetry.