Catalytic mechanism of Kdo8P synthase: transient kinetic studies and evaluation of a putative reaction intermediate

The mechanistic pathway for the reaction catalyzed by Kdo8P synthase has been investigated, and the cyclic bisphosphate 2 has been examined as a putative reaction intermediate. Two parallel approaches were used: (1) chemical synthesis of 2 and evaluation as an alternate substrate for the enzyme and (2) transient kinetic studies using rapid chemical quench methodology to provide direct observation and characterization of putative intermediate(s) during enzyme catalysis. The putative cyclic bisphosphate intermediate 2, possessing the stereochemistry of the beta-pyranose form, was synthesized and evaluated as a substrate and as an inhibitor of Kdo8P synthase. The substrate activity was examined by monitoring the release of anomeric phosphate over time using proton-decoupled 31P NMR spectroscopy. A very similar time course for the formation of inorganic phosphate was found in each experiment and the corresponding control experiment; i.e., no enzyme-catalyzed acceleration in the anomeric phosphate hydrolysis was detected. It was found however that 2 binds to the enzyme and is a competitive inhibitor with respect to phosphoenolpyruvate binding, having a Ki value of 35 microM. In a parallel study, we have performed single-turnover rapid chemical quench experiments to examine both the forward and reverse directions to identify a putative enzyme intermediate(s). Our results clearly demonstrate that the cyclic bisphosphate intermediate 2 does not accumulate under single-enzyme turnover conditions. This observation, coupled with the results obtained through the evaluation of synthetic 2 as a substrate, strongly suggests that the Kdo8P synthase catalytic pathway does not involve the formation of 2 as a reaction intermediate. Taken together, these combined results support the original hypothesis [Hedstrom, L., and Abeles, R. H. (1988) Biochem. Biophys. Res. Commun. 157, 816-820], which suggests a reaction pathway involving an acyclic bisphosphate intermediate 1.     

Kinetic competence of a phosphoryl enzyme intermediate in the glucose-1,6-p2 synthase-catalyzed reaction. Purification, properties, and kinetic studies

Glucose-1,6-P2 synthase of beef brain which catalyzes the formation of glucose-1,6-P2 and glycerate-3-P from glycerate-1,3-P2 and glucose-1-P has been purified 700-fold with an overall recovery of 19%. The purification procedure involves an ammonium sulfate fractionation of the crude extract, DE52 and hydroxylapatite column chromatography and isoelectric focusing. The isolated enzyme appears to be homogeneous by sodium dodecyl sulfate gel electrophoresis. Its molecular weight is estimated to be about 70,000 by gel filtration on Sephadex G-200 which agrees with the value obtained by sodium dodecyl sulfate gel electrophoresis. A phosphoryl enzyme intermediate in the catalytic reaction is indicated by the following evidence: glycerate-1,3-P2[1-32P] labels the enzyme. The label is removed by acceptor substrates such as glucose-1-P. Using a rapid quenching device at 23 degrees and pH 8.0, the first order rate constant for phosphorylation of the enzyme is 20 s-1, compared with an overall rate with the best acceptor, glucose-1-P, of 19 s-1. Dephosphorylation by glucose-1-P is at 37 s-1. Mg2+ is required for both phosphoryl transfers and the overall reaction. In the complete reaction the fraction of enzyme that is phosphorylated depends on the concentrations of glycerate-1,3-P2 and the concentration and nature of the acceptor in a way that could be predicted from the steady state parameters, the Km values, and the kinetic constants observed for the single turnover. Reciprocal plots of initial rates as a function of both substrate concentrations are families of parallel lines. The 32P-labeled phosphoryl enzyme intermediate was found to be acid-stable and somewhat alkaline-labile. Phosphoserine was identified from the partial acid hydrolysate of a protease digest of [32P] phosphoryl enzyme by two-dimensional thin layer chromatography.     

Simulation of S2-state multiline EPR signal in oriented photosystem II membranes: structural implications for the manganese cluster in an oxygen-evolving complex

High-quality angular-dependent spectra of multiline electron paramagnetic resonance (EPR) signals from the S2-state Mn cluster in a photosynthetic oxygen-evolving complex (OEC) were obtained for partially oriented photosystem (PS) II membranes, and the magnetic structure of the Mn cluster has been studied by simulation analysis. The angular-dependent multiline spectra were simulated by taking into account the anisotropic properties of both hyperfine tensors of intrinsic Mn ions and g-tensor of the cluster in a tetranuclear model. The best-fit parameters for the simulation indicate that (a) the oxidation state of the S2-state Mn cluster is Mn(III, IV, IV, IV), (b) the electronic orbital configuration of the Mn(III) ion is (dpi)3[dz2(sigma))]1, (c) the effective g-tensor of the Mn cluster and the hyperfine tensor of the Mn(III) ion are axially symmetric, and their principal z-axes are nearly collinear each other, and (d) the z-axis of the dz2 orbital of the Mn(III) ion and the normal of the thylakoid membrane are at an angle of 50.1 +/- 1.8 degrees. The results are compatible with those of the oriented XAFS study [Mukerji, I., et al. (1994) Biochemistry 33, 9712-9721], and indicate that the O-O vector of the putative di-mu-oxo bridged Mn(III)-Mn(IV) dimer unit in the Mn cluster tilts by 43-56 degrees with respect to the normal of thylakoid membrane. A model of the arrangement of the di-mu-oxo bridged Mn(III)-Mn(IV) unit with respect to the thylakoid membrane is proposed.     

Time-resolved EPR studies with DNA photolyase: excited-state FADH0 abstracts an electron from Trp-306 to generate FADH-, the catalytically active form of the cofactor

Photolyase repairs UV-induced cyclobutane-pyrimidine dimers in DNA by photoinduced electron transfer. The enzyme isolated from Escherichia coli contains 5,10-methenyltetrahydrofolate, which functions as the light-harvesting chromophore, and fully reduced flavin adenine dinucleotide (FAD), which functions as the redox catalyst. During enzyme preparation, the flavin is oxidized to FADH0, which is catalytically inert. Illumination of the enzyme with 300- to 600-nm light converts the flavin to the fully reduced form in a reaction that involves photooxidation of an amino acid in the apoenzyme. The results of earlier optical studies had indicated that the redox-active amino acid in this photoactivation process was tryptophan. We have now used time-resolved electron paramagnetic resonance (EPR) spectroscopy to investigate the photoactivation reaction. Excitation of the flavin-radical-containing inactive enzyme produces a spin-polarized radical that we identify by 2H and 15N labeling as originating from a tryptophan residue, confirming the inferences from the optical work. These results and Trp-->Phe replacement by site-directed mutagenesis reveal that flavin radical photoreduction is achieved by electron abstraction from Trp-306 by the excited-state FADH0. Analysis of the hyperfine couplings and spin density distribution deduced from the isotopic-labeling results shows that the product of the light-driven redox chemistry is the Trp-306 cation radical. The results strongly suggest that the active form of photolyase contains FADH- and not FADH2.     

Role of the GroEL chaperonin intermediate domain in coupling ATP hydrolysis to polypeptide release

Modification of the Escherichia coli chaperonin GroEL with N-ethylmaleimide at residue Cys138 affects the structural and functional integrity of the complex. Nucleotide affinity and ATPase activity of the modified chaperonin are increased, whereas cooperativity of ATP hydrolysis and affinity for GroES are reduced. As a consequence, release and folding of substrate proteins are strongly impaired and uncoupled from ATP hydrolysis in a temperature-dependent manner. Folding of dihydrofolate reductase at 25 degrees C becomes dependent on GroES, whereas folding of typically GroES-dependent proteins is blocked completely. At 37 degrees C, GroES binding is restored to normal levels, and the modified GroEL regains its chaperone activity to some extent. These results assign a central role to the intermediate GroEL domain for transmitting conformational changes between apical and central domains, and for coupling ATP hydrolysis to productive protein release.     

The role of the reactions of .NO with superoxide and oxygen in biological systems: a kinetic approach

In this study we calculate the half-life of .NO in its reactions with superoxide and with oxygen under various conditions using the known rate constants for these reactions. The measured half-life of .NO in biological systems is 3-5 s, which agrees well with the calculated value for intracellular .NO, but not for extracellular .NO under normal physiological conditions. The autoxidation of .NO to yield NO2- as a final product cannot be responsible for such a short measured half-life under normal as well as pathologic conditions. Therefore, if there is direct evidence for the occurrence of the reaction of .NO with O2.- in the medium, one has to assume that the steady state concentrations of free .NO are much lower than those measured. The very low concentrations of free .NO in biological systems may result from its reversible strong binding to biological molecules. Simulation of the mechanism of the autoxidation of .NO indicates that the binding constants of .NO to O2 or to another .NO are too small to account for the very low concentration of free .NO in biological systems. Nevertheless, the reaction of .NO with oxygen cannot be neglected in biological systems if the intermediate ONOO. reacts rapidly with a biological target. The biological damage caused by ONOO. is expected to be due to the radical itself and to peroxynitrite, which is most probably formed via the reaction of ONOO. with the biological molecule.