Low Resolution Structure of Yeast Phosphoglycerate Kinase

Yeast phosphoglycerate kinase, like the same enzyme from horse muscle, has two structural lobes, reminiscent of a dimer rather than a monomer.     

Yeast tRNAAsp-Aspartyl-tRNA Synthetase Complex: Low Resolution Crystal Structure

Abstract

Yeast aspartyl-tRNA synthetase, a dimer of molecular weight 125000, and two molecules of its cognate tRNA (M_r = 24160) cocrystallize in the cubic space group 1432 (a = 354 Å). The crystal structure was solved to low resolution using neutron and X-ray diffraction data. Neutron single crystal diffraction data were collected in five solvents differing by their D₂O content in order to use the contrast variation method to distinguish between the protein and tRNA The synthetase was first located at 40 Å resolution using the 65% D₂O neutron data (tRNA matched). tRNA molecules were found at 20 Å resolution using both neutron and X-ray data. The resulting model was refined against 10 Å resolution X-ray data, using density modification and least-squares refinement of the tRNA positions. The crystal structure, solved without a priori phase knowledge, was confirmed later by isomorphous replacement. The molecular model of the complex is in good agreement with results obtained in solution by probing the protected part of the tRNA by chemical reagents.     

植物iPGAM的研究进展

辅因子非依赖型磷酸甘油酸变位酶(Cofactor-independent phosphoglycerate mutase,iPGAM)是在真菌和高等植物中发现的金属酶,是糖酵解和糖异生过程中的一个关键酶。随着原核生物、无脊椎动物等物种中iPGAM基因被克隆、蛋白晶体结构的解析及其生物学功能的陆续报道,近些年,植物iPGAM的功能开始受到关注。阐述了植物iPGAM蛋白的结构特点及作用机制,着重对已报道的拟南芥、水稻和玉米中iPGAMs的系统进化关系以及生物学功能进行了概述。     

Structure of Horse-muscle Phosphoglycerate Kinase at 6 Å Resolution

The single peptide chain of 3-phosphoglycerate kinase is folded into two distinct globular units, only one of which seems to be involved in substrate binding.     

Studies on Crystalline Yeast Phosphoglyceric Acid Mutase

In order to study the properties of crystalline phosphoglyceric acid mutase, the polarimetric method was employed for the direct measurement of the enzyme activity. As a result, it was found that the enzyme was inhibited by various metallic ions, chelating agents and phosphoryl enolpyruvate, but not influenced by SH-inhibitors. In addition, fluoride was found to inhibit the enzyme activity in a special manner. Some observations on the basic properties are also presented.     

Studies on Crystalline Yeast Phosphoglycenc Acid Mutase

Effects of pH and some chemical agents (1) on the solubilization of insoluble pectin bound to suspended particles, (2) on the viscosity decrease of native soluble pectin, (3) on the flocculation of suspended particles and (4) on the over-all clarification of apple juice have been studied Optimum pH ranges were: (1), 3.2~4.0; (2), 3.6~4.1; (3), lower than 3.0; (4), 3.2~3.8. Gelatin had no effect on (1) and (2) but stimulated (3) and (4). NaCl had no detectable effect on (2) and (3) but slightly stimulated (1) and (4). CaCl₂ strongly inhibited (1), (2) and (3). SnCl₄ stimulated (3) but strongly inhibited (1), (2) and (4). EDTA (ethylenediamineteraacetic acid) accelerated (1) and (4), and had no detectable effect on (2) and (3).     

Kinetic Studies on Crystalline Yeast Phosphoglyceric Acid Mutase

Effects of the substrate and the coenzyme on the crystalline yeast phosphoglyceric acid mutase activity have been investigated. Lineweaver-Burk plots at different concentrations of the substrate (d-3-phosphoglyceric acid: 3×10^?7 to 8×10^?3m) and the coenzyme (d-2, 3-diphosphoglyceric acid: 8×10^?7 to 10^?5m) change in such a way to indicate the involvement of an enzyme-substrate-coenzyme ternary complex as an active intermediate in the enzymic reaction process. It is concluded that the reaction catalyzed by the yeast enzyme follows the sequential pathway and that a phosphorylated enzyme does not participate as an obligatory intermediate in the reaction mechanism, if it occurs. Kinetic studies indicate Km values of 6×10^?4m for d-3-phosphoglyceric acid and 8×10^?7m for d-2, 3-diphosphoglyceric acid. The substrate is a competitive inhibitor of the coenzyme with a Ksi (inhibition constant) of 3.2×10^?3m. The coenzyme inhibition is not observed at concentration tested. A kinetic treatment to determine the mechanism of the enzyme reaction from the experimental data which are obtaind in the range of inhibitory substrate concentrations is presented.     

A Conserved Motif Mediates both Multimer Formation and Allosteric Activation of Phosphoglycerate Mutase 5

Phosphoglycerate mutase 5 (PGAM5) is an atypical mitochondrial Ser/Thr phosphatase that modulates mitochondrial dynamics and participates in both apoptotic and necrotic cell death. The mechanisms that regulate the phosphatase activity of PGAM5 are poorly understood. The C-terminal phosphoglycerate mutase domain of PGAM5 shares homology with the catalytic domains found in other members of the phosphoglycerate mutase family, including a conserved histidine that is absolutely required for catalytic activity. However, this conserved domain is not sufficient for maximal phosphatase activity. We have identified a highly conserved amino acid motif, WDXNWD, located within the unique N-terminal region, which is required for assembly of PGAM5 into large multimeric complexes. Alanine substitutions within the WDXNWD motif abolish the formation of multimeric complexes and markedly reduce phosphatase activity of PGAM5. A peptide containing the WDXNWD motif dissociates the multimeric complex and reduces but does not fully abolish phosphatase activity. Addition of the WDXNWD-containing peptide in trans to a mutant PGAM5 protein lacking the WDXNWD motif markedly increases phosphatase activity of the mutant protein. Our results are consistent with an intermolecular allosteric regulation mechanism for the phosphatase activity of PGAM5, in which the assembly of PGAM5 into multimeric complexes, mediated by the WDXNWD motif, results in maximal activation of phosphatase activity. Our results suggest the possibility of identifying small molecules that function as allosteric regulators of the phosphatase activity of PGAM5.     

Reversible Dissociation of Crystalline Yeast Phosphoglyceric Acid Mutase in Alkali

The structure of crystalline yeast phosphoglyceric acid mutase has been investigated by sedimentation-velocity and equilibrium measurements, optical rotatory dispersion measurements and viscometry. The data indicate that this enzyme is a globular, compact and highly organized protein with a low helix content. The native structure remains unchanged at pH 10.5. Dissociation of the enzyme into subunits has been observed at pH values of 11.5 and above. From optical rotatory dispersion measurements, it is found that the enzyme loses a large part of its organized conformation when it dissociates in alkaline solution. On neutralization, the alkali-treated enzyme regains its activity. The ability to regain the enzyme activity is gradually lowered with the increase of pH value to be incubated and with time of exposure. Inactivation at pH 13.0 is almost irreversible. However, the reversibility of the inactivation at pH 13.0 is appreciably enhanced by the presence of phosphate compounds in the reactivation system. Particulary, it is found that presence of substrates or the coenzyme is effective for considerable improvement of the reversibility. Molecular weight analyses by ultracentrifugation indicate that subunits have approximately equal molecular weights and that the native enzyme is consisted of four polypeptide chains.     

抗肿瘤代谢靶标磷酸甘油酸变位酶1 及其抑制剂的研究进展

肿瘤细胞的Warburg效应是近期肿瘤代谢研究的一大热点,磷酸甘油酸变位酶1（PGAM1）在糖酵解生物通路中起着重要作用。 报道显示PGAM1在肿瘤细胞中普遍高表达,同时促进细胞增殖过程中的糖酵解和生物合成代谢通路。基于该发现,针对PGAM1进行小 分子抑制剂研究成为开发抗肿瘤药物的新思路。综述PGAM1在肿瘤细胞中的功能、意义以及PGAM1抑制剂的开发前景。     

Cofactor-Independent Phosphoglycerate Mutase from Nematodes Has Limited Druggability,as Revealed by Two High-Throughput Screens

Cofactor-independent phosphoglycerate mutase (iPGAM) is essential for the growth of C. elegans but is absent from humans, suggesting its potential as a drug target in parasitic nematodes such as Brugia malayi, a cause of lymphatic filariasis (LF). iPGAM''s active site is small and hydrophilic, implying that it may not be druggable, but another binding site might permit allosteric inhibition. As a comprehensive assessment of iPGAM''s druggability, high-throughput screening (HTS) was conducted at two different locations: ∼220,000 compounds were tested against the C. elegans iPGAM by Genzyme Corporation, and ∼160,000 compounds were screened against the B. malayi iPGAM at the National Center for Drug Screening in Shanghai. iPGAM''s catalytic activity was coupled to downstream glycolytic enzymes, resulting in NADH consumption, as monitored by a decline in visible-light absorbance at 340 nm. This assay performed well in both screens (Z′-factor >0.50) and identified two novel inhibitors that may be useful as chemical probes. However, these compounds have very modest potency against the B. malayi iPGAM (IC₅₀ >10 µM) and represent isolated singleton hits rather than members of a common scaffold. Thus, despite the other appealing properties of the nematode iPGAMs, their low druggability makes them challenging to pursue as drug targets. This study illustrates a “druggability paradox” of target-based drug discovery: proteins are generally unsuitable for resource-intensive HTS unless they are considered druggable, yet druggability is often difficult to predict in the absence of HTS data.     

Low Resolution Structure of Glyceraldehyde 3-Phosphate Dehydrogenase

The structure of the holo enzyme shows that the four chemically identical sub-units are arranged with almost perfect 222 symmetry. There are indications, however, that the active centre regions might only be related in pairs.     

Crystal Structures of Leishmania mexicana Phosphoglycerate Mutase Suggest a One-Metal Mechanism and a New Enzyme Subclass

The structures of Leishmania mexicana cofactor-independent phosphoglycerate mutase (Lm iPGAM) crystallised with the substrate 3-phosphoglycerate at high and low cobalt concentrations have been solved at 2.00- and 1.90-Å resolutions. Both structures are very similar and the active site contains both 3-phosphoglycerate and 2-phosphoglycerate at equal occupancies (50%). Lm iPGAM co-crystallised with the product 2-phosphoglycerate yields the same structure. Two Co²⁺ are coordinated within the active site with different geometries and affinities. The cobalt at the M1 site has a distorted octahedral geometry and is present at 100% occupancy. The M2-site Co²⁺ binds with distorted tetrahedral geometry, with only partial occupancy, and coordinates with Ser75, the residue involved in phosphotransfer. When the M2 site is occupied, the side chain of Ser75 adopts a position that is unfavourable for catalysis, indicating that this site may not be occupied under physiological conditions and that catalysis may occur via a one-metal mechanism. The geometry of the M2 site suggests that it is possible for Ser75 to be activated for phosphotransfer by H-bonding to nearby residues rather than by metal coordination. The 16 active-site residues of Lm iPGAM are conserved in the Mn-dependent iPGAM from Bacillus stearothermophilus (33% overall sequence identity). However, Lm iPGAM has an inserted tyrosine (Tyr210) that causes the M2 site to diminish in size, consistent with its reduced metal affinity. Tyr210 is present in trypanosomatid and plant iPGAMs, but not in the enzymes from other organisms, indicating that there are two subclasses of iPGAMs.     

Persistent Overexpression of Phosphoglycerate Mutase,a Glycolytic Enzyme,Modifies Energy Metabolism and Reduces Stress Resistance of Heart in Mice

Background

Heart failure is associated with changes in cardiac energy metabolism. Glucose metabolism in particular is thought to be important in the pathogenesis of heart failure. We examined the effects of persistent overexpression of phosphoglycerate mutase 2 (Pgam2), a glycolytic enzyme, on cardiac energy metabolism and function.

Methods and Results

Transgenic mice constitutively overexpressing Pgam2 in a heart-specific manner were generated, and cardiac energy metabolism and function were analyzed. Cardiac function at rest was normal. The uptake of analogs of glucose or fatty acids and the phosphocreatine/βATP ratio at rest were normal. A comprehensive metabolomic analysis revealed an increase in the levels of a few metabolites immediately upstream and downstream of Pgam2 in the glycolytic pathway, whereas the levels of metabolites in the initial few steps of glycolysis and lactate remained unchanged. The levels of metabolites in the tricarboxylic acid (TCA) cycle were altered. The capacity for respiration by isolated mitochondria in vitro was decreased, and that for the generation of reactive oxygen species (ROS) in vitro was increased. Impaired cardiac function was observed in response to dobutamine. Mice developed systolic dysfunction upon pressure overload.

Conclusions

Constitutive overexpression of Pgam2 modified energy metabolism and reduced stress resistance of heart in mice.     

Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 Å Resolution

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Phosphoglycerate Mutase 1 Promotes Cell Proliferation and Neuroblast Differentiation in the Dentate Gyrus by Facilitating the Phosphorylation of cAMP Response Element-Binding Protein

Neurochemical Research - In a previous study, we observed a significant increase in phosphoglycerate mutase 1 (PGAM1) levels after pyridoxine treatment. In the present study, we investigated the...     

Conformational Transitions in Yeast Chorismate Mutase Important for Allosteric Regulation as Identified by Nuclear Magnetic Resonance Spectroscopy

Proteins fluctuate between different conformations in solution, and these conformational fluctuations can be important for protein function and allosteric regulation. The chorismate mutase from Saccharomyces cerevisiae (ScCM), a key enzyme in the biosynthesis of aromatic amino acids, is allosterically activated and inhibited by tryptophan and tyrosine, respectively. It was initially proposed that in the absence of effector, ScCM fluctuates between activated R and inhibited T conformations according to the Monod-Wyman-Changeux (MWC) model, although a more complex regulation pattern was later suggested by mutagenesis and kinetic data. Here we used NMR relaxation dispersion experiments to understand the conformational fluctuations on the microsecond-to-millisecond timescale that occur in ScCM. In the absence of allosteric effectors, ScCM did not exclusively exchange between T and R conformations, suggesting that the two-state MWC model is insufficient to explain conformational dynamics. Addition of tyrosine led to the quenching of much of the motion on this timescale, while new motions were identified in the presence of tryptophan. These new motions are consistent with conformational fluctuations into an alternative conformation that may be important for enzyme activity.