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1.
Protein Sci ; 33(7): e5075, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38895978

ABSTRACT

Rheostat positions, which can be substituted with various amino acids to tune protein function across a range of outcomes, are a developing area for advancing personalized medicine and bioengineering. Current methods cannot accurately predict which proteins contain rheostat positions or their substitution outcomes. To compare the prevalence of rheostat positions in homologs, we previously investigated their occurrence in two pyruvate kinase (PYK) isozymes. Human liver PYK contained numerous rheostat positions that tuned the apparent affinity for the substrate phosphoenolpyruvate (Kapp-PEP) across a wide range. In contrast, no functional rheostat positions were identified in Zymomonas mobilis PYK (ZmPYK). Further, the set of ZmPYK substitutions included an unusually large number that lacked measurable activity. We hypothesized that the inactive substitution variants had reduced protein stability, precluding detection of Kapp-PEP tuning. Using modified buffers, robust enzymatic activity was obtained for 19 previously-inactive ZmPYK substitution variants at three positions. Surprisingly, both previously-inactive and previously-active substitution variants all had Kapp-PEP values close to wild-type. Thus, none of the three positions were functional rheostat positions, and, unlike human liver PYK, ZmPYK's Kapp-PEP remained poorly tunable by single substitutions. To directly assess effects on stability, we performed thermal denaturation experiments for all ZmPYK substitution variants. Many diminished stability, two enhanced stability, and the three positions showed different thermal sensitivity to substitution, with one position acting as a "stability rheostat." The differences between the two PYK homologs raises interesting questions about the underlying mechanism(s) that permit functional tuning by single substitutions in some proteins but not in others.


Subject(s)
Pyruvate Kinase , Zymomonas , Humans , Zymomonas/enzymology , Zymomonas/genetics , Zymomonas/chemistry , Zymomonas/metabolism , Pyruvate Kinase/chemistry , Pyruvate Kinase/metabolism , Pyruvate Kinase/genetics , Amino Acid Substitution , Protein Stability , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Enzyme Stability , Liver/enzymology , Liver/metabolism , Liver/chemistry , Phosphoenolpyruvate/metabolism , Phosphoenolpyruvate/chemistry
2.
Talanta ; 275: 126134, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38692044

ABSTRACT

Phosphoenolpyruvate (PEP) is an essential intermediate metabolite that is involved in various vital biochemical reactions. However, achieving the direct and accurate quantification of PEP in plasma or serum poses a significant challenge owing to its strong polarity and metal affinity. In this study, a sensitive method for the direct determination of PEP in plasma and serum based on ethylenediaminetetraacetic acid (EDTA)-facilitated hydrophilic interaction liquid chromatography-tandem mass spectrometry was developed. Superior chromatographic retention and peak shapes were achieved using a zwitterionic stationary-phase HILIC column with a metal-inert inner surface. Efficient dechelation of PEP-metal complexes in serum/plasma samples was achieved through the introduction of EDTA, resulting in a significant enhancement of the PEP signal. A PEP isotopically labelled standard was employed as a surrogate analyte for the determination of endogenous PEP, and validation assessments proved the sensitivity, selectivity, and reproducibility of this method. The method was applied to the comparative quantification of PEP in plasma and serum samples from mice and rats, as well as in HepG2 cells, HEK293T cells, and erythrocytes; the results confirmed its applicability in PEP-related biomedical research. The developed method can quantify PEP in diverse biological matrices, providing a feasible opportunity to investigate the role of PEP in relevant biomedical research.


Subject(s)
Edetic Acid , Hydrophobic and Hydrophilic Interactions , Phosphoenolpyruvate , Tandem Mass Spectrometry , Tandem Mass Spectrometry/methods , Animals , Humans , Edetic Acid/chemistry , Mice , Chromatography, Liquid/methods , Rats , Phosphoenolpyruvate/chemistry , Phosphoenolpyruvate/blood , Phosphoenolpyruvate/metabolism , HEK293 Cells , Hep G2 Cells , Rats, Sprague-Dawley , Male
3.
J Mol Biol ; 436(9): 168553, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38548260

ABSTRACT

The catalytic cycle of Enzyme I (EI), a phosphotransferase enzyme responsible for converting phosphoenolpyruvate (PEP) into pyruvate, is characterized by a series of local and global conformational rearrangements. This multistep process includes a monomer-to-dimer transition, followed by an open-to-closed rearrangement of the dimeric complex upon PEP binding. In the present study, we investigate the thermodynamics of EI dimerization using a range of high-pressure solution NMR techniques complemented by SAXS experiments. 1H-15N TROSY and 1H-13C methyl TROSY NMR spectra combined with 15N relaxation measurements revealed that a native-like engineered variant of full-length EI fully dissociates into stable monomeric state above 1.5 kbar. Conformational ensembles of EI monomeric state were generated via a recently developed protocol combining coarse-grained molecular simulations with experimental backbone residual dipolar coupling measurements. Analysis of the structural ensembles provided detailed insights into the molecular mechanisms driving formation of the catalytically competent dimeric state, and reveals that each step of EI catalytical cycle is associated with a significant reduction in either inter- or intra-domain conformational entropy. Altogether, this study completes a large body work conducted by our group on EI and establishes a comprehensive structural and dynamical description of the catalytic cycle of this prototypical multidomain, oligomeric enzyme.


Subject(s)
Phosphoenolpyruvate Sugar Phosphotransferase System , Phosphotransferases (Nitrogenous Group Acceptor) , Protein Multimerization , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Phosphoenolpyruvate/metabolism , Phosphoenolpyruvate/chemistry , Phosphoenolpyruvate Sugar Phosphotransferase System/chemistry , Phosphotransferases (Nitrogenous Group Acceptor)/chemistry , Protein Conformation , Scattering, Small Angle , Thermodynamics , X-Ray Diffraction
4.
Chembiochem ; 23(20): e202200285, 2022 10 19.
Article in English | MEDLINE | ID: mdl-35943842

ABSTRACT

Phosphonates are produced across all domains of life and used widely in medicine and agriculture. Biosynthesis almost universally originates from the enzyme phosphoenolpyruvate mutase (Ppm), EC 5.4.2.9, which catalyzes O-P bond cleavage in phosphoenolpyruvate (PEP) and forms a high energy C-P bond in phosphonopyruvate (PnPy). Mechanistic scrutiny of this unusual intramolecular O-to-C phosphoryl transfer began with the discovery of Ppm in 1988 and concluded in 2008 with computational evidence supporting a concerted phosphoryl transfer via a dissociative metaphosphate-like transition state. This mechanism deviates from the standard 'in-line attack' paradigm for enzymatic phosphoryl transfer that typically involves a phosphoryl-enzyme intermediate, but definitive evidence is sparse. Here we review the experimental evidence leading to our current mechanistic understanding and highlight the roles of previously underappreciated conserved active site residues. We then identify remaining opportunities to evaluate overlooked residues and unexamined substrates/inhibitors.


Subject(s)
Organophosphonates , Phosphotransferases (Phosphomutases) , Phosphoenolpyruvate/chemistry , Phosphotransferases (Phosphomutases)/chemistry , Catalysis
5.
Acta Crystallogr F Struct Biol Commun ; 78(Pt 4): 177-184, 2022 Apr 01.
Article in English | MEDLINE | ID: mdl-35400670

ABSTRACT

A structure-function characterization of Synechococcus elongatus enolase (SeEN) is presented, representing the first structural report on a cyanobacterial enolase. X-ray crystal structures of SeEN in its apoenzyme form and in complex with phosphoenolpyruvate are reported at 2.05 and 2.30 Šresolution, respectively. SeEN displays the typical fold of enolases, with a conformationally flexible loop that closes the active site upon substrate binding, assisted by two metal ions that stabilize the negatively charged groups. The enzyme exhibits a catalytic efficiency of 1.2 × 105 M-1 s-1 for the dehydration of 2-phospho-D-glycerate, which is comparable to the kinetic parameters of related enzymes. These results expand the understanding of the biophysical features of these enzymes, broadening the toolbox for metabolic engineering applications.


Subject(s)
Phosphopyruvate Hydratase , Synechococcus , Crystallography, X-Ray , Phosphoenolpyruvate/chemistry , Phosphopyruvate Hydratase/chemistry
6.
Protein Sci ; 30(9): 1833-1853, 2021 09.
Article in English | MEDLINE | ID: mdl-34076313

ABSTRACT

When amino acids vary during evolution, the outcome can be functionally neutral or biologically-important. We previously found that substituting a subset of nonconserved positions, "rheostat" positions, can have surprising effects on protein function. Since changes at rheostat positions can facilitate functional evolution or cause disease, more examples are needed to understand their unique biophysical characteristics. Here, we explored whether "phylogenetic" patterns of change in multiple sequence alignments (such as positions with subfamily specific conservation) predict the locations of functional rheostat positions. To that end, we experimentally tested eight phylogenetic positions in human liver pyruvate kinase (hLPYK), using 10-15 substitutions per position and biochemical assays that yielded five functional parameters. Five positions were strongly rheostatic and three were non-neutral. To test the corollary that positions with low phylogenetic scores were not rheostat positions, we combined these phylogenetic positions with previously-identified hLPYK rheostat, "toggle" (most substitution abolished function), and "neutral" (all substitutions were like wild-type) positions. Despite representing 428 variants, this set of 33 positions was poorly statistically powered. Thus, we turned to the in vivo phenotypic dataset for E. coli lactose repressor protein (LacI), which comprised 12-13 substitutions at 329 positions and could be used to identify rheostat, toggle, and neutral positions. Combined hLPYK and LacI results show that positions with strong phylogenetic patterns of change are more likely to exhibit rheostat substitution outcomes than neutral or toggle outcomes. Furthermore, phylogenetic patterns were more successful at identifying rheostat positions than were co-evolutionary or eigenvector centrality measures of evolutionary change.


Subject(s)
Amino Acid Substitution , DNA/chemistry , Escherichia coli Proteins/chemistry , Evolution, Molecular , Lac Repressors/chemistry , Pyruvate Kinase/chemistry , Adenosine Diphosphate/chemistry , Adenosine Diphosphate/metabolism , Binding Sites , Cloning, Molecular , Computational Biology/methods , DNA/genetics , DNA/metabolism , Escherichia coli/classification , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Gene Expression , Genetic Vectors/chemistry , Genetic Vectors/metabolism , Humans , Kinetics , Lac Repressors/genetics , Lac Repressors/metabolism , Models, Molecular , Mutation , Phosphoenolpyruvate/chemistry , Phosphoenolpyruvate/metabolism , Phylogeny , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Pyruvate Kinase/genetics , Pyruvate Kinase/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Structure-Activity Relationship , Thermodynamics
7.
Arch Biochem Biophys ; 695: 108633, 2020 11 30.
Article in English | MEDLINE | ID: mdl-33075302

ABSTRACT

A linked-function theory for allostery allows for a differentiation between those protein-ligand interactions that contribute the most to ligand binding and those protein-ligand interactions that contribute to the allosteric mechanism. This potential distinction is the basis for analogue studies used to determine which chemical moieties on the allosteric effector contribute to allostery. Although less recognized, the same separation of functions is possible for substrate-enzyme interactions. When evaluating allosteric regulation in human liver pyruvate kinase, the use of a range of monovalent cations (K+, NH4+, Rb+, Cs+, cyclohexylammonium+ and Tris+) altered substrate (phosphoenolpyruvate; PEP) affinity, but maintained similar allosteric responses to the allosteric activator, fructose-1,6-bisphosphate (Fru-1,6-BP). Because crystal structures indicate that the active site monovalent cation interacts directly with the phosphate moiety of the bound PEP substrate, we questioned if the phosphate moiety might contribute to substrate binding, but not to the allosteric mechanism. Here, we demonstrate that the binding of oxalate, a non-phosphorylated substrate/product analogue, is allosterically enhanced by Fru-1,6-BP. That observation is consistent with the concept that the phosphate moiety of PEP is not required for the allosteric function, even though that moiety likely contributes to determining substrate affinity.


Subject(s)
Fructosediphosphates/chemistry , Liver/enzymology , Phosphoenolpyruvate/chemistry , Pyruvate Kinase/chemistry , Allosteric Regulation , Fructosediphosphates/metabolism , Humans , Phosphoenolpyruvate/metabolism , Pyruvate Kinase/metabolism
8.
Biochem J ; 477(11): 2095-2114, 2020 06 12.
Article in English | MEDLINE | ID: mdl-32459324

ABSTRACT

Activation of phosphoenolpyruvate carboxylase (PEPC) enzymes by glucose 6-phosphate (G6P) and other phospho-sugars is of major physiological relevance. Previous kinetic, site-directed mutagenesis and crystallographic results are consistent with allosteric activation, but the existence of a G6P-allosteric site was questioned and competitive activation-in which G6P would bind to the active site eliciting the same positive homotropic effect as the substrate phosphoenolpyruvate (PEP)-was proposed. Here, we report the crystal structure of the PEPC-C4 isozyme from Zea mays with G6P well bound into the previously proposed allosteric site, unambiguously confirming its existence. To test its functionality, Asp239-which participates in a web of interactions of the protein with G6P-was changed to alanine. The D239A variant was not activated by G6P but, on the contrary, inhibited. Inhibition was also observed in the wild-type enzyme at concentrations of G6P higher than those producing activation, and probably arises from G6P binding to the active site in competition with PEP. The lower activity and cooperativity for the substrate PEP, lower activation by glycine and diminished response to malate of the D239A variant suggest that the heterotropic allosteric activation effects of free-PEP are also abolished in this variant. Together, our findings are consistent with both the existence of the G6P-allosteric site and its essentiality for the activation of PEPC enzymes by phosphorylated compounds. Furthermore, our findings suggest a central role of the G6P-allosteric site in the overall kinetics of these enzymes even in the absence of G6P or other phospho-sugars, because of its involvement in activation by free-PEP.


Subject(s)
Glucose-6-Phosphate/chemistry , Phosphoenolpyruvate Carboxylase/chemistry , Phosphoenolpyruvate/chemistry , Plant Proteins/chemistry , Zea mays/enzymology , Allosteric Regulation , Catalytic Domain , Glucose-6-Phosphate/metabolism , Kinetics , Phosphoenolpyruvate/metabolism , Phosphoenolpyruvate Carboxylase/genetics , Phosphoenolpyruvate Carboxylase/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Zea mays/genetics
9.
Biochim Biophys Acta Proteins Proteom ; 1868(1): 140296, 2020 01.
Article in English | MEDLINE | ID: mdl-31676451

ABSTRACT

Entamoeba histolytica infection is highly prevalent in developing countries across the globe. The ATP synthesis in this pathogen is solely dependent on the glycolysis pathway where pyruvate kinase (Pyk) catalyzes the final reaction. Here, we have cloned, overexpressed and purified the pyruvate kinase (EhPyk) from E. histolytica. EhPyk is the shortest currently known Pyk till date as it contains only two of the three characterized domains when compared to the other homologues and our phylogenetic analysis places it on a distinct branch from the known type I/II Pyks. Our purification results suggested that it exists as a homodimer in solution. The kinetic characterization showed that EhPyk has maximum activity at pH 7.5 where it exhibited Michaelis-Menten's kinetics for phosphoenolpyruvate with a Km of 0.23 mM, and it lost its activity at both the acidic pH 4.0 and basic pH 10.0. We also determined the key secondary structural elements of EhPyk at different pH values. MD simulation of EhPyk structure at different pH values suggested that it is most stable at pH 7.0, while least stable at pH 10.0 followed by pH 4.0. Together, our computational simulations correlate well with the experimental studies. In summary, this study expands the current understanding of the EhPyk identified earlier in the amoebic genome and provides the first characterization of this bacterially expressed protein.


Subject(s)
Entamoeba histolytica/enzymology , Protozoan Proteins/chemistry , Pyruvate Kinase/chemistry , Enzyme Stability , Escherichia coli/genetics , Hydrogen-Ion Concentration , Molecular Dynamics Simulation , Phosphoenolpyruvate/chemistry , Phylogeny , Protozoan Proteins/genetics , Pyruvate Kinase/genetics
10.
Biochemistry ; 58(35): 3669-3682, 2019 09 03.
Article in English | MEDLINE | ID: mdl-31386812

ABSTRACT

Cancer cells regulate key enzymes in the glycolytic pathway to control the glycolytic flux, which is necessary for their growth and proliferation. One of the enzymes is pyruvate kinase muscle isoform 2 (PKM2), which is allosterically regulated by various small molecules. Using detailed biochemical and kinetic studies, we demonstrate that cysteine inhibits wild-type (wt) PKM2 by shifting from an active tetramer to a mixture of a tetramer and a less active dimer/monomer equilibrium and that the inhibition is dependent on cysteine concentration. The cysteine-mediated PKM2 inhibition is reversed by fructose 1,6-bisphosphate, an allosteric activator of PKM2. Furthermore, kinetic studies using two dimeric PKM2 variants, S437Y PKM2 and G415R PKM2, show that the reversal is caused by the tetramerization of wtPKM2. The crystal structure of the wtPKM2-Cys complex was determined at 2.25 Å, which showed that cysteine is held to the amino acid binding site via its main chain groups, similar to that observed for phenylalanine, alanine, serine, and tryptophan. Notably, ligand binding studies using fluorescence and isothermal titration calorimetry show that the presence of phosphoenolpyruvate alters the binding affinities of amino acids for wtPKM2 and vice versa, thereby unravelling the existence of a functionally bidirectional coupling between the amino acid binding site and the active site of wtPKM2.


Subject(s)
Carrier Proteins/antagonists & inhibitors , Carrier Proteins/chemistry , Cysteine/pharmacology , Enzyme Inhibitors/pharmacology , Membrane Proteins/antagonists & inhibitors , Membrane Proteins/chemistry , Thyroid Hormones/chemistry , Amino Acid Substitution/genetics , Amino Acids/chemistry , Amino Acids/metabolism , Carrier Proteins/genetics , Carrier Proteins/metabolism , Catalysis , Catalytic Domain/genetics , Crystallography, X-Ray , Humans , Isoenzymes/antagonists & inhibitors , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Ligands , Membrane Proteins/genetics , Membrane Proteins/metabolism , Models, Molecular , Mutant Proteins/antagonists & inhibitors , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Phosphoenolpyruvate/chemistry , Phosphoenolpyruvate/metabolism , Protein Binding , Protein Conformation , Serine/genetics , Thyroid Hormones/genetics , Thyroid Hormones/metabolism , Tyrosine/genetics , Thyroid Hormone-Binding Proteins
11.
Nat Commun ; 10(1): 1558, 2019 04 05.
Article in English | MEDLINE | ID: mdl-30952857

ABSTRACT

Cofactor F420 plays critical roles in primary and secondary metabolism in a range of bacteria and archaea as a low-potential hydride transfer agent. It mediates a variety of important redox transformations involved in bacterial persistence, antibiotic biosynthesis, pro-drug activation and methanogenesis. However, the biosynthetic pathway for F420 has not been fully elucidated: neither the enzyme that generates the putative intermediate 2-phospho-L-lactate, nor the function of the FMN-binding C-terminal domain of the γ-glutamyl ligase (FbiB) in bacteria are known. Here we present the structure of the guanylyltransferase FbiD and show that, along with its archaeal homolog CofC, it accepts phosphoenolpyruvate, rather than 2-phospho-L-lactate, as the substrate, leading to the formation of the previously uncharacterized intermediate dehydro-F420-0. The C-terminal domain of FbiB then utilizes FMNH2 to reduce dehydro-F420-0, which produces mature F420 species when combined with the γ-glutamyl ligase activity of the N-terminal domain. These new insights have allowed the heterologous production of F420 from a recombinant F420 biosynthetic pathway in Escherichia coli.


Subject(s)
Biosynthetic Pathways , Escherichia coli/metabolism , Riboflavin/analogs & derivatives , Models, Molecular , Nucleotidyltransferases/chemistry , Nucleotidyltransferases/metabolism , Phosphoenolpyruvate/chemistry , Phosphoenolpyruvate/metabolism , Prokaryotic Cells/metabolism , Riboflavin/biosynthesis
12.
J Biotechnol ; 267: 19-28, 2018 Feb 10.
Article in English | MEDLINE | ID: mdl-29301095

ABSTRACT

Indirubin is an indole alkaloid that can be used to treat various diseases including granulocytic leukemia, cancer, and Alzheimer's disease. Microbial production of indirubin has so far been achieved by supplementation of rather expensive substrates such as indole or tryptophan. Here, we report the development of metabolically engineered Escherichia coli strain capable of producing indirubin directly from glucose. First, the Methylophaga aminisulfidivorans flavin-containing monooxygenase (FMO) and E. coli tryptophanase (TnaA) were introduced into E. coli in order to complete the biosynthetic pathway from tryptophan to indirubin. Further engineering was performed through rational strategies including disruption of the regulatory repressor gene trpR and removal of feedback inhibitions on AroG and TrpE. Then, combinatorial approach was employed by systematically screening eight genes involved in the common aromatic amino acid pathway. Moreover, availability of the aromatic precursor substrates, phosphoenolpyruvate and erythrose-4-phosphate, was enhanced by inactivating the pykF (pyruvate kinase I) and pykA (pyruvate kinase II) genes, and by overexpressing the tktA gene (encoding transketolase), respectively. Fed-batch fermentation of the final engineered strain led to production of 0.056 g/L of indirubin directly from glucose. The metabolic engineering and synthetic biology strategies reported here thus allows microbial fermentative production of indirubin from glucose.


Subject(s)
Metabolic Engineering , Oxygenases/genetics , Tryptophanase/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Escherichia coli/enzymology , Escherichia coli/genetics , Glucose/biosynthesis , Glucose/chemistry , Indoles/chemistry , Indoles/metabolism , Metabolic Engineering/methods , Oxygenases/metabolism , Phosphoenolpyruvate/chemistry , Piscirickettsiaceae/enzymology , Pyruvate Kinase/chemistry , Pyruvate Kinase/genetics , Repressor Proteins/genetics , Repressor Proteins/metabolism , Substrate Specificity , Transketolase/chemistry , Transketolase/genetics
13.
Protein Sci ; 26(8): 1667-1673, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28470715

ABSTRACT

Pyruvate phosphate dikinase (PPDK) is an essential enzyme of both the C4 photosynthetic pathway and cellular energy metabolism of some bacteria and unicellular protists. In C4 plants, it catalyzes the ATP- and Pi -dependent formation of phosphoenolpyruvate (PEP) while in bacteria and protozoa the ATP-forming direction is used. PPDK is composed out of three distinct domains and exhibits one of the largest single domain movements known today during its catalytic cycle. However, little information about potential intermediate steps of this movement was available. A recent study resolved a discrete intermediate step of PPDK's swiveling movement, shedding light on the details of this intriguing mechanism. Here we present an additional structural intermediate that possibly represents another crucial step in the catalytic cycle of PPDK, providing means to get a more detailed understanding of PPDK's mode of function.


Subject(s)
Flaveria/chemistry , Phosphoenolpyruvate/chemistry , Plant Proteins/chemistry , Pyruvate, Orthophosphate Dikinase/chemistry , Biocatalysis , Catalytic Domain , Cloning, Molecular , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Flaveria/enzymology , Gene Expression , Models, Molecular , Phosphoenolpyruvate/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Domains , Pyruvate, Orthophosphate Dikinase/genetics , Pyruvate, Orthophosphate Dikinase/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity , Thermodynamics
14.
Sci Rep ; 7: 45389, 2017 03 30.
Article in English | MEDLINE | ID: mdl-28358005

ABSTRACT

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.


Subject(s)
Flaveria/enzymology , Plant Proteins/metabolism , Pyruvate, Orthophosphate Dikinase/metabolism , Binding Sites , Catalytic Domain , Crystallography, X-Ray , Molecular Dynamics Simulation , Phosphoenolpyruvate/chemistry , Phosphoenolpyruvate/metabolism , Plant Proteins/chemistry , Principal Component Analysis , Protein Conformation , Pyruvate, Orthophosphate Dikinase/chemistry , Pyruvate, Orthophosphate Dikinase/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification
15.
Nat Chem ; 9(4): 310-317, 2017 04.
Article in English | MEDLINE | ID: mdl-28338685

ABSTRACT

Phosphoenol pyruvate is the highest-energy phosphate found in living organisms and is one of the most versatile molecules in metabolism. Consequently, it is an essential intermediate in a wide variety of biochemical pathways, including carbon fixation, the shikimate pathway, substrate-level phosphorylation, gluconeogenesis and glycolysis. Triose glycolysis (generation of ATP from glyceraldehyde 3-phosphate via phosphoenol pyruvate) is among the most central and highly conserved pathways in metabolism. Here, we demonstrate the efficient and robust synthesis of phosphoenol pyruvate from prebiotic nucleotide precursors, glycolaldehyde and glyceraldehyde. Furthermore, phosphoenol pyruvate is derived within an α-phosphorylation controlled reaction network that gives access to glyceric acid 2-phosphate, glyceric acid 3-phosphate, phosphoserine and pyruvate. Our results demonstrate that the key components of a core metabolic pathway central to energy transduction and amino acid, sugar, nucleotide and lipid biosyntheses can be reconstituted in high yield under mild, prebiotically plausible conditions.


Subject(s)
Evolution, Chemical , Glycolysis , Origin of Life , Phosphoenolpyruvate/chemistry , Trioses/chemistry , Molecular Structure , Phosphorylation
16.
Biochemistry ; 56(4): 592-601, 2017 01 31.
Article in English | MEDLINE | ID: mdl-28045507

ABSTRACT

3-Deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthase catalyzes an aldol-like reaction of phosphoenolpyruvate (PEP) with erythrose 4-phosphate (E4P) to form DAHP in the first step of the shikimate biosynthetic pathway. DAHP oxime, in which an oxime replaces the ketone, is a potent inhibitor, with Ki = 1.5 µM. Linear free energy relationship (LFER) analysis of DAHP oxime inhibition using DAHP synthase mutants revealed an excellent correlation between transition state stabilization and inhibition. The equations of LFER analysis were rederived to formalize the possibility of proportional, rather than equal, changes in the free energies of transition state stabilization and inhibitor binding, in accord with the fact that the majority of LFER analyses in the literature demonstrate nonunity slopes. A slope of unity, m = 1, indicates that catalysis and inhibitor binding are equally sensitive to perturbations such as mutations or modified inhibitor/substrate structures. Slopes <1 or >1 indicate that inhibitor binding is less sensitive or more sensitive, respectively, to perturbations than is catalysis. LFER analysis using the tetramolecular specificity constant, that is, plotting log(KM,MnKM,PEPKM,E4P/kcat) versus log(Ki), revealed a slope, m, of 0.34, with r2 = 0.93. This provides evidence that DAHP oxime is mimicking the first irreversible transition state of the DAHP synthase reaction, presumably phosphate departure from the tetrahedral intermediate. This is evidence that the oxime group can act as a functional, as well as structural, mimic of phosphate groups.


Subject(s)
3-Deoxy-7-Phosphoheptulonate Synthase/antagonists & inhibitors , Bacterial Proteins/antagonists & inhibitors , Enzyme Inhibitors/chemistry , Oximes/chemistry , Recombinant Fusion Proteins/chemistry , Sugar Phosphates/chemistry , 3-Deoxy-7-Phosphoheptulonate Synthase/chemistry , 3-Deoxy-7-Phosphoheptulonate Synthase/genetics , 3-Deoxy-7-Phosphoheptulonate Synthase/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Biocatalysis , Cloning, Molecular , Escherichia coli/genetics , Escherichia coli/metabolism , Kinetics , Models, Molecular , Molecular Mimicry , Mutation , Phosphoenolpyruvate/chemistry , Phosphoenolpyruvate/metabolism , Protein Binding , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Shikimic Acid/chemistry , Shikimic Acid/metabolism , Sugar Phosphates/metabolism , Thermodynamics
17.
Arch Biochem Biophys ; 607: 1-6, 2016 10 01.
Article in English | MEDLINE | ID: mdl-27477958

ABSTRACT

The allosteric coupling free energy between ligands fructose-6-phosphate (Fru-6-P) and phospho(enol)pyruvate (PEP) for phosphofructokinase-1 (PFK) from the moderate thermophile, Bacillus stearothermophilus (BsPFK), results from compensating enthalpy and entropy components. In BsPFK the positive coupling free energy that defines inhibition is opposite in sign from the negative enthalpy term and is therefore determined by the larger absolute value of the negative entropy term. Variants of BsPFK were made to determine the effect of adding small cavities to the structure on the allosteric function of the enzyme. The BsPFK Ile → Val (cavity containing) mutants have varied values for the coupling free energy between PEP and Fru-6-P, indicating that the modifications altered the effectiveness of PEP as an inhibitor. Notably, the mutation I153V had a substantial positive impact on the magnitude of inhibition by PEP. Van't Hoff analysis determined that this is the result of decreased entropy-enthalpy compensation with a larger change in the enthalpy term compared to the entropy term.


Subject(s)
Bacterial Proteins/chemistry , Geobacillus stearothermophilus/enzymology , Phosphofructokinases/chemistry , Allosteric Site , Bacterial Proteins/genetics , Catalysis , Crystallography, X-Ray , Fructosephosphates/chemistry , Geobacillus stearothermophilus/genetics , Hydrogen-Ion Concentration , Kinetics , Molecular Conformation , Mutagenesis, Site-Directed , Mutation , Phosphoenolpyruvate/chemistry , Phosphofructokinases/genetics , Temperature
18.
Arch Biochem Biophys ; 606: 26-33, 2016 09 15.
Article in English | MEDLINE | ID: mdl-27431058

ABSTRACT

Although oxidative stress is known to impede the tricarboxylic acid (TCA) cycle and oxidative phosphorylation, the nutritionally-versatile microbe, Pseudomonas fluorescens has been shown to proliferate in the presence of hydrogen peroxide (H2O2) and nitrosative stress. In this study we demonstrate the phospho-transfer system that enables this organism to generate ATP was similar irrespective of the carbon source utilized. Despite the diminished activities of enzymes involved in the TCA cycle and in the electron transport chain (ETC), the ATP levels did not appear to be significantly affected in the stressed cells. Phospho-transfer networks mediated by acetate kinase (ACK), adenylate kinase (AK), and nucleoside diphosphate kinase (NDPK) are involved in maintaining ATP homeostasis in the oxidatively-challenged cells. This phospho-relay machinery orchestrated by substrate-level phosphorylation is aided by the up-regulation in the activities of such enzymes like phosphoenolpyruvate carboxylase (PEPC), pyruvate orthophosphate dikinase (PPDK), and phosphoenolpyruvate synthase (PEPS). The enhanced production of phosphoenolpyruvate (PEP) and pyruvate further fuel the synthesis of ATP. Taken together, this metabolic reconfiguration enables the organism to fulfill its ATP need in an O2-independent manner by utilizing an intricate phospho-wire module aimed at maximizing the energy potential of PEP with the participation of AMP.


Subject(s)
Adenosine Triphosphate/chemistry , Pseudomonas fluorescens/metabolism , Adenosine Monophosphate/chemistry , Citric Acid Cycle , Densitometry , Electron Transport , Homeostasis , Hydrogen Peroxide/chemistry , Lipids/chemistry , Oxidation-Reduction , Oxidative Phosphorylation , Oxidative Stress , Oxygen/chemistry , Phosphoenolpyruvate/chemistry , Phosphorylation , Phosphotransferases (Paired Acceptors)/metabolism , Pyruvate, Orthophosphate Dikinase/metabolism , Reactive Oxygen Species/metabolism
19.
Acta Crystallogr D Biol Crystallogr ; 71(Pt 12): 2457-70, 2015 Dec 01.
Article in English | MEDLINE | ID: mdl-26627653

ABSTRACT

Staphylococcus aureus is a Gram-positive bacterium with strong pathogenicity that causes a wide range of infections and diseases. Enolase is an evolutionarily conserved enzyme that plays a key role in energy production through glycolysis. Additionally, enolase is located on the surface of S. aureus and is involved in processes leading to infection. Here, crystal structures of Sa_enolase with and without bound phosphoenolpyruvate (PEP) are presented at 1.6 and 2.45 Šresolution, respectively. The structure reveals an octameric arrangement; however, both dimeric and octameric conformations were observed in solution. Furthermore, enzyme-activity assays show that only the octameric variant is catalytically active. Biochemical and structural studies indicate that the octameric form of Sa_enolase is enzymatically active in vitro and likely also in vivo, while the dimeric form is catalytically inactive and may be involved in other biological processes.


Subject(s)
Bacterial Proteins/chemistry , Phosphoenolpyruvate/chemistry , Phosphopyruvate Hydratase/chemistry , Staphylococcus aureus/chemistry , Amino Acid Motifs , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Kinetics , Models, Molecular , Molecular Sequence Data , Phosphoenolpyruvate/metabolism , Phosphopyruvate Hydratase/genetics , Phosphopyruvate Hydratase/metabolism , Protein Binding , Protein Multimerization , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Staphylococcus aureus/enzymology
20.
Int J Mol Sci ; 16(7): 14490-510, 2015 Jun 25.
Article in English | MEDLINE | ID: mdl-26121302

ABSTRACT

Streptococcus iniae is a major fish pathogen that can also cause human bacteremia, cellulitis and meningitis. Screening for and identification of protective antigens plays an important role in developing therapies against S. iniae infections. In this study, we indicated that the α-enolase of S. iniae was not only distributed in the cytoplasm and associated to cell walls, but was also secreted to the bacterial cell surface. The functional identity of the purified recombinant α-enolase protein was verified by its ability to catalyze the conversion of 2-phosphoglycerate (2-PGE) to phosphoenolpyruvate (PEP), and both the recombinant and native proteins interacted with human plasminogen. The rabbit anti-rENO serum blockade assay shows that α-enolase participates in S. iniae adhesion to and invasion of BHK-21 cells. In addition, the recombinant α-enolase can confer effective protection against S. iniae infection in mice, which suggests that α-enolase has potential as a vaccine candidate in mammals. We conclude that S. iniae α-enolase is a moonlighting protein that also associates with the bacterial outer surface and functions as a protective antigen in mice.


Subject(s)
Antigens, Bacterial/immunology , Bacterial Outer Membrane Proteins/metabolism , Phosphopyruvate Hydratase/metabolism , Streptococcus/enzymology , Amino Acid Sequence , Animals , Bacterial Outer Membrane Proteins/chemistry , Bacterial Outer Membrane Proteins/genetics , Bacterial Outer Membrane Proteins/immunology , Cell Adhesion , Cell Line , Cell Movement , Cloning, Molecular , Cricetinae , Cricetulus , Glyceric Acids/chemistry , Mice , Molecular Sequence Data , Phosphoenolpyruvate/chemistry , Phosphopyruvate Hydratase/chemistry , Phosphopyruvate Hydratase/genetics , Phosphopyruvate Hydratase/immunology , Streptococcus/genetics , Streptococcus/immunology
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