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1.
Arch Biochem Biophys ; 711: 109017, 2021 10 30.
Article in English | MEDLINE | ID: mdl-34411580

ABSTRACT

A previous study showed that 2'-3'-O-(2,4,6-trinitrophenyl) adenosine 5'-triphosphate (TNP-ATP) was a weak allosteric activator of Rhizobium etli pyruvate carboxylase (RePC) in the absence of acetyl-CoA. On the other hand, TNP-ATP inhibited the allosteric activation of RePC by acetyl-CoA. Here, we aimed to study the role of triphosphate group of TNP-ATP on its allosteric activation of the enzyme and inhibition of acetyl-CoA-dependent activation of RePC using TNP-ATP and its derivatives, including TNP-ADP, TNP-AMP and TNP-adenosine. The pyruvate carboxylation activity was assayed to determine the effect of reducing the number of phosphate groups in TNP-ATP derivatives on allosteric activation and inhibition of acetyl-CoA activation of RePC and chicken liver pyruvate carboxylase (CLPC). Reducing the number of phosphate groups in TNP-ATP derivatives decreased the activation efficacy for both RePC and CLPC compared to TNP-ATP. The apparent binding affinity and inhibition of activation of the enzymes by acetyl-CoA were also diminished when the number of phosphate groups in the TNP-ATP derivatives was reduced. Whilst TNP-AMP activated RePC, it did not activate CLPC, but it did inhibit acetyl-CoA activation of both RePC and CLPC. Similarly, TNP-adenosine did not activate RePC; however, it did inhibit acetyl-CoA activation using a different mechanism compared to phosphorylated TNP-derivatives. These findings indicate that mechanisms of PC activation and inhibition of acetyl-CoA activation by TNP-ATP and its derivatives are different. This study provides the basis for possible drug development for treatment of metabolic diseases and cancers with aberrant expression of PC.


Subject(s)
Acetyl Coenzyme A/chemistry , Adenosine Triphosphate/analogs & derivatives , Allosteric Regulation/drug effects , Enzyme Activators/chemistry , Pyruvate Carboxylase/chemistry , Adenosine Diphosphate/analogs & derivatives , Adenosine Diphosphate/chemistry , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/chemistry , Adenosine Triphosphate/chemistry , Animals , Chickens , Enzyme Assays , Kinetics , Liver/enzymology , Molecular Structure
2.
Adv Exp Med Biol ; 1286: 15-48, 2021.
Article in English | MEDLINE | ID: mdl-33725343

ABSTRACT

Several studies have exploited the metabolic hallmarks that distinguish between normal and cancer cells, aiming at identifying specific targets of anti-cancer drugs. It has become apparent that metabolic flexibility allows cancer cells to survive during high anabolic demand or the depletion of nutrients and oxygen. Cancers can reprogram their metabolism to the microenvironments by increasing aerobic glycolysis to maximize ATP production, increasing glutaminolysis and anabolic pathways to support bioenergetic and biosynthetic demand during rapid proliferation. The increased key regulatory enzymes that support the relevant pathways allow us to design small molecules which can specifically block activities of these enzymes, preventing growth and metastasis of tumors. In this review, we discuss metabolic adaptation in cancers and highlight the crucial metabolic enzymes involved, specifically those involved in aerobic glycolysis, glutaminolysis, de novo fatty acid synthesis, and bioenergetic pathways. Furthermore, we also review the success and the pitfalls of the current anti-cancer drugs which have been applied in pre-clinical and clinical studies.


Subject(s)
Antineoplastic Agents , Neoplasms , Antineoplastic Agents/therapeutic use , Citric Acid Cycle , Energy Metabolism , Glycolysis , Humans , Neoplasms/drug therapy , Tumor Microenvironment
3.
Arch Biochem Biophys ; 695: 108630, 2020 11 30.
Article in English | MEDLINE | ID: mdl-33080172

ABSTRACT

The formation, kinetics and thermodynamic activation parameters of hybrid tetramers of pyruvate carboxylase (PC) formed between wild-type Rhizobium etli pyruvate carboxylase (WTRePC) and mutant forms of this enzyme, as well as between Aspergillus nidulans PC and mutant forms of RePC have been characterized in a previous study. In this current work, we aim to extend the previous study by forming hybrid tetramers between WTRePC or chicken liver PC (CLPC) with single or double mutant RePCs. By forming hybrid tetramers between WTRePC with either K1119A or ΔBCCP RePC, the biotin moiety and BCCP (biotin carboxyl carrier protein) domain appear to play a crucial role in determination of thermodynamic activation parameters, especially the activation entropy, and the order of tetrameric structure. Using E218A:K1119A hybrid tetramers, an alternative pathway of biotin carboxylation occurred only in the absence of acetyl CoA. In this pathway, the biotin of the E218A subunits is carboxylated in the BC domain of the K1119A subunits, since the E218A mutation destroys the catalytic activity of the BC domain. Transfer of the carboxyl group to pyruvate could then occur in the CT domain of either E218A or K1119A. Part of the reduction of activity in hybrid tetramers of WTRePC and double mutant, E218A.K1119A could result from the loss of this pathway. Previously, D1018A mutant RePC homotetramers exhibited a 12-fold increase in the rate constant for catalysis in the absence of acetyl CoA. This was taken to indicate that inter-residue interactions involving D1018 inhibit the interconversion between the symmetrical and asymmetrical forms of the tetramer in the absence of acetyl CoA. The mutation, D1018A, in hybrid tetramers of WTRePC:D1018A.K1119A (D1018A.K1119A is a double mutant form of RePC) had no such effect on the rate constant, suggesting that in hybrid tetramers obligatory oscillation between asymmetrical and symmetrical conformers of the tetramer is not required to drive the catalytic cycle. Finally, K1119A or E218A RePC mutant can form hybrid tetramers with PC subunits from an evolutionarily distant species, chicken, that have stability characteristics that lie between those of the homotetramers of the two enzymes. This work provides insights into the how the PC tetramer functions to perform catalysis and is regulated by acetyl CoA. The ability to form hybrid tetrameric PCs composed of PC subunits from widely varying species that have a mixture of characteristics of the two source enzymes may also provide ways of developing novel PCs for biotechnological purposes.


Subject(s)
Aspergillus nidulans , Avian Proteins/chemistry , Bacterial Proteins/chemistry , Biotin/chemistry , Chickens , Fungal Proteins/chemistry , Liver/enzymology , Pyruvate Carboxylase/chemistry , Rhizobium etli , Animals , Aspergillus nidulans/enzymology , Aspergillus nidulans/genetics , Avian Proteins/genetics , Avian Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biotin/genetics , Biotin/metabolism , Catalysis , Fungal Proteins/genetics , Fungal Proteins/metabolism , Protein Domains , Protein Structure, Quaternary , Pyruvate Carboxylase/genetics , Pyruvate Carboxylase/metabolism , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Rhizobium etli/enzymology , Rhizobium etli/genetics
4.
Methods Mol Biol ; 2077: 51-61, 2020.
Article in English | MEDLINE | ID: mdl-31707651

ABSTRACT

The method described in this chapter provides a quantitative means of assaying for protein histidine phosphorylation and thus protein histidine kinase activity, even in the presence of other protein kinases, for example, serine/threonine or tyrosine kinases. The method involves the measurement of 32P, derived from [γ32P]ATP, incorporation into phosphohistidine in a protein substrate. The method makes use of the differential stabilities of phosphohistidine and the common phosphohydroxyamino acids to alkali and acid treatments to measure phosphohistidine incorporation. Phosphoserine and phosphothreonine are depleted by alkali treatment, while phosphohistidine, which is alkali-stable, is removed by acid treatment. Phosphotyrosine is stable to both alkali and acid treatments. The method is filter-based and allows for rapid assay of multiple protein histidine kinase samples, for example, screening for histidine kinase activity, allowing for the calculation of specific activity. In addition, quantitative time-course assays can also be performed to allow for kinetic analysis of histidine kinase activity.


Subject(s)
Biological Assay , Histidine/metabolism , Proteins/metabolism , Adenosine Triphosphate/metabolism , Animals , Biological Assay/methods , Histidine/analogs & derivatives , Histidine Kinase/metabolism , Histones/metabolism , Phosphorylation , Proteins/chemistry , Rats
5.
Arch Biochem Biophys ; 665: 87-95, 2019 04 15.
Article in English | MEDLINE | ID: mdl-30831071

ABSTRACT

In sedimentation velocity experiments, we have been able to detect hybrid Rhizobium etli pyruvate carboxylase tetramers formed between subunits that contain covalently bound biotin and mutant subunits that do not. This was performed by forming complexes of the tetramers with the biotin-binding protein avidin. In addition, we have shown that it is possible to form hybrid tetramers of pyruvate carboxylase subunits from two different organisms (bacteria - Rhizobium etli and fungi - Aspergillus nidulans). In hybrid tetramers containing mutant subunits that are not fully catalytically active and fully catalytically active subunits, the catalytic and regulatory properties of these hybrid tetramers are modified compared to homotetramers of the fully active pyruvate carboxylase subunits. Our data indicates that the model of catalysis involving half-of-the-sites activity in which there is obligatory alternation of pyruvate carboxylating activity between pairs of subunits either face of the tetramer, does not occur in the hybrid tetramers. Our results are also discussed in relation to recent findings that there are multiple pathways of biotin carboxylation and decarboxylation between subunits in pyruvate carboxylase tetramers.


Subject(s)
Biopolymers/metabolism , Pyruvate Carboxylase/metabolism , Thermodynamics , Allosteric Regulation , Avidin/metabolism , Biopolymers/chemistry , Catalysis , Kinetics , Pyruvate Carboxylase/chemistry , Ultracentrifugation
6.
J Mol Med (Berl) ; 96(3-4): 237-247, 2018 04.
Article in English | MEDLINE | ID: mdl-29362846

ABSTRACT

Pyruvate carboxylase (PC), an anaplerotic enzyme, plays an essential role in various cellular metabolic pathways including gluconeogenesis, de novo fatty acid synthesis, amino acid synthesis, and glucose-induced insulin secretion. Deregulation of PC expression or activity has long been known to be associated with metabolic syndrome in several rodent models. Accumulating data in the past decade clearly showed that deregulation of PC expression is associated with type 2 diabetes in humans, while targeted inhibition of PC expression in a mouse model reduced adiposity and improved insulin sensitivity in diet-induced type 2 diabetes. More recent studies also show that PC is strongly involved in tumorigenesis in several cancers, including breast, non-small cell lung cancer, glioblastoma, renal carcinoma, and gall bladder. Systems metabolomics analysis of these cancers identified pyruvate carboxylation as an essential metabolic hub that feeds carbon skeletons of downstream metabolites of oxaloacetate into the biosynthesis of various cellular components including membrane lipids, nucleotides, amino acids, and the redox control. Inhibition or down-regulation of PC expression in several cancers markedly impairs their growth ex vivo and in vivo, drawing attention to PC as an anti-cancer target. PC has also exhibited a moonlight function by interacting with immune surveillance that can either promote or block viral infection. In certain pathogenic bacteria, PC is essential for infection, replication, and maintenance of their virulence phenotype.


Subject(s)
Diabetes Mellitus/metabolism , Infections/metabolism , Neoplasms/metabolism , Pyruvate Carboxylase/metabolism , Animals , Humans , Pyruvic Acid/metabolism
7.
Biochem Mol Biol Educ ; 46(2): 130-140, 2018 03.
Article in English | MEDLINE | ID: mdl-29285862

ABSTRACT

Assessment is a central component of course curriculums and is used to certify student learning, but it can also be used as a tool to improve teaching and learning. Many laboratory courses are structured such that there is only a grade for a particular laboratory, which limits the insights that can be gained in student learning. We developed a laboratory program that incorporates assessments designed to probe student understanding of different components of the individual modules making up the program. The challenge was to analyze and present grades from these assessment tasks in a format that was readily interpretable by academics. We show that a simplified synthesis of grade distributions (grade distribution digests) provides sufficient information to make decisions about changes in course components. The main feature of the digests is its data visualization approach, where student grades for individual laboratory practicals, individual assessment tasks or individual assessment items are graphically presented as an overall average grade, an average top quartile grade and an average bottom quartile grade, and relative averages across all assessments. This ability to visualize student grades in variety of contexts enables academics with many other demands on their time (e.g. research and administration) to more efficiently identify ways to improve teaching delivery and learning outcomes. Examples are presented of the use of such data to identify and improve deficiencies in both student skills and teaching practice, resulting in improved learning outcomes. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(2):130-140, 2018.


Subject(s)
Educational Measurement , Laboratories , Learning , Teaching/education , Humans , Students , Universities
8.
Lab Invest ; 98(3): 283-290, 2018 03.
Article in English | MEDLINE | ID: mdl-29200201

ABSTRACT

Nucleoside diphosphate kinases (NDPKs) are multifunctional proteins encoded by the nme (non-metastatic cells) genes, also called NM23. NDPKs catalyze the transfer of γ-phosphate from nucleoside triphosphates to nucleoside diphosphates by a ping-pong mechanism involving the formation of a high-energy phosphohistidine intermediate. Growing evidence shows that NDPKs, particularly NDPK-B, can additionally act as a protein histidine kinase. Protein kinases and phosphatases that regulate reversible O-phosphorylation of serine, threonine, and tyrosine residues have been studied extensively in many organisms. Interestingly, other phosphoamino acids histidine, lysine, arginine, aspartate, glutamate, and cysteine exist in abundance but remain understudied due to the paucity of suitable methods and antibodies. The N-phosphorylation of histidine by histidine kinases via the two- or multi-component signaling systems is an important mediator in cellular responses in prokaryotes and lower eukaryotes, like yeast, fungi, and plants. However, in vertebrates knowledge of phosphohistidine signaling has lagged far behind and the identity of the protein kinases and protein phosphatases involved is not well established. This article will therefore provide an overview of our current knowledge on protein histidine phosphorylation particularly the role of nm 23 gene products as protein histidine kinases.


Subject(s)
NM23 Nucleoside Diphosphate Kinases/metabolism , Animals , Calcium Channels/metabolism , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , GTP-Binding Proteins/metabolism , Histidine Kinase/metabolism , Humans , Neoplasm Metastasis , Phosphorylation , Potassium Channels, Calcium-Activated/metabolism
9.
Amino Acids ; 49(8): 1309-1323, 2017 08.
Article in English | MEDLINE | ID: mdl-28578504

ABSTRACT

The synthesis and chemistry of the lesser-known phosphoamino acids, O-phosphohydroxylysine, O-phosphohydroxyproline, N 1-phosphotryptophan and S-phosphocysteine are described in detail. In addition, where anything at all is known, the biological synthesis, occurrence and functions of these phosphoamino acids are described. Of these phosphoamino acids, only N 1-phosphotryptophan has not been reported to occur in proteins; however, apart from the roles of S-phosphocysteine in the sugar transporter component (EII) and in catalysis by protein phosphotyrosine phosphatase, little is currently known about the biological roles of the phosphoamino acids when they occur as post-translational modifications.


Subject(s)
Phosphoamino Acids/chemistry , Protein Processing, Post-Translational , Proteins/chemistry , Animals , Cysteine/analogs & derivatives , Cysteine/chemistry , Humans , Hydroxylysine/analogs & derivatives , Hydroxylysine/chemistry , Phosphorylation
10.
Biochemistry ; 55(30): 4220-8, 2016 08 02.
Article in English | MEDLINE | ID: mdl-27379711

ABSTRACT

The mechanism of allosteric activation of pyruvate carboxylase by acetyl CoA is not fully understood. Here we have examined the roles of residues near the acetyl CoA binding site in the allosteric activation of Rhizobium etli pyruvate carboxylase using site-directed mutagenesis. Arg429 was found to be especially important for acetyl CoA binding as substitution with serine resulted in a 100-fold increase in the Ka of acetyl CoA activation and a large decrease in the cooperativity of this activation. Asp420 and Arg424, which do not make direct contact with bound acetyl CoA, were nonetheless found to affect acetyl CoA binding when mutated, probably through changed interactions with another acetyl CoA binding residue, Arg427. Thermodynamic activation parameters for the pyruvate carboxylation reaction were determined from modified Arrhenius plots and showed that acetyl CoA acts to decrease the activation free energy of the reaction by both increasing the activation entropy and decreasing the activation enthalpy. Most importantly, mutations of Asp420, Arg424, and Arg429 enhanced the activity of the enzyme in the absence of acetyl CoA. A main focus of this work was the detailed investigation of how this increase in activity occurred in the R424S mutant. This mutation decreased the activation enthalpy of the pyruvate carboxylation reaction by an amount consistent with removal of a single hydrogen bond. It is postulated that Arg424 forms a hydrogen bonding interaction with another residue that stabilizes the asymmetrical conformation of the R. etli pyruvate carboxylase tetramer, constraining its interconversion to the symmetrical conformer that is required for catalysis.


Subject(s)
Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Pyruvate Carboxylase/chemistry , Pyruvate Carboxylase/metabolism , Rhizobium etli/enzymology , Acetyl Coenzyme A/metabolism , Allosteric Regulation , Allosteric Site/genetics , Amino Acid Sequence , Arginine/chemistry , Aspartic Acid/chemistry , Bacterial Proteins/genetics , Enzyme Activation , Glutamic Acid/chemistry , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Protein Conformation , Pyruvate Carboxylase/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Rhizobium etli/genetics
11.
Front Pharmacol ; 6: 173, 2015.
Article in English | MEDLINE | ID: mdl-26347652

ABSTRACT

Reversible phosphorylation of amino acid side chains in proteins is a frequently used mechanism in cellular signal transduction and alterations of such phosphorylation patterns are very common in cardiovascular diseases. They reflect changes in the activities of the protein kinases and phosphatases involving signaling pathways. Phosphorylation of serine, threonine, and tyrosine residues has been extensively investigated in vertebrates, whereas reversible histidine phosphorylation, a well-known regulatory signal in lower organisms, has been largely neglected as it has been generally assumed that histidine phosphorylation is of minor importance in vertebrates. More recently, it has become evident that the nucleoside diphosphate kinase isoform B (NDPK-B), an ubiquitously expressed enzyme involved in nucleotide metabolism, and a highly specific phosphohistidine phosphatase (PHP) form a regulatory histidine protein kinase/phosphatase system in mammals. At least three well defined substrates of NDPK-B are known: The ß-subunit of heterotrimeric G-proteins (Gß), the intermediate conductance potassium channel SK4 and the Ca(2+) conducting TRP channel family member, TRPV5. In each of these proteins the phosphorylation of a specific histidine residue regulates cellular signal transduction or channel activity. This article will therefore summarize our current knowledge on protein histidine phosphorylation and highlight its relevance for cardiovascular physiology and pathophysiology.

12.
FEBS Lett ; 589(16): 2073-9, 2015 Jul 22.
Article in English | MEDLINE | ID: mdl-26149215

ABSTRACT

We have examined the roles of Asp1018, Glu1027, Arg469 and Asp471 in the allosteric domain of Rhizobium etli pyruvate carboxylase. Arg469 and Asp471 interact directly with the allosteric activator acetyl coenzyme A (acetyl CoA) and the R469S and R469K mutants showed increased enzymic activity in the presence and absence of acetyl CoA, whilst the D471A mutant exhibited no acetyl CoA-activation. E1027A, E1027R and D1018A mutants had increased activity in the absence of acetyl CoA, but not in its presence. These results suggest that most of these residues impose restrictions on the structure and/or dynamics of the enzyme to affect activity.


Subject(s)
Acetyl Coenzyme A/metabolism , Bacterial Proteins/metabolism , Models, Molecular , Pyruvate Carboxylase/metabolism , Rhizobium etli/enzymology , Acetyl Coenzyme A/chemistry , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Allosteric Regulation , Allosteric Site , Amino Acid Substitution , Arginine/chemistry , Aspartic Acid/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bicarbonates/chemistry , Biocatalysis , Glutamic Acid/chemistry , Kinetics , Magnesium/chemistry , Molecular Conformation , Mutagenesis, Site-Directed , Mutant Proteins/chemistry , Mutant Proteins/metabolism , Protein Stability , Pyruvate Carboxylase/chemistry , Pyruvate Carboxylase/genetics , Pyruvic Acid/chemistry , Pyruvic Acid/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Rhizobium etli/metabolism
13.
Anal Biochem ; 485: 102-8, 2015 Sep 15.
Article in English | MEDLINE | ID: mdl-26073659

ABSTRACT

Cholesterol oxidase (CO) is a FAD (flavin adenine dinucleotide) containing enzyme that catalyzes the oxidization and isomerization of cholesterol. Studies directed toward elucidating the catalytic mechanism of CO will provide an important general understanding of Flavin-assisted redox catalysis. Hydrogen atoms play an important role in enzyme catalysis; however, they are not readily visualized in protein X-ray diffraction structures. Neutron crystallography is an ideal method for directly visualizing hydrogen positions at moderate resolutions because hydrogen and deuterium have comparable neutron scattering lengths to other heavy atoms present in proteins. The negative coherent and large incoherent scattering lengths of hydrogen atoms in neutron diffraction experiments can be circumvented by replacing hydrogen atoms with its isotope, deuterium. The perdeuterated form of CO was successfully expressed from minimal medium, purified, and crystallized. X-ray crystallographic structures of the enzyme in the perdeuterated and hydrogenated states confirm that there are no apparent structural differences between the two enzyme forms. Kinetic assays demonstrate that perdeuterated and hydrogenated enzymes are functionally identical. Together, structural and functional studies indicate that the perdeuterated protein is suitable for structural studies by neutron crystallography directed at understanding the role of hydrogen atoms in enzyme catalysis.


Subject(s)
Cholesterol Oxidase/chemistry , Deuterium/chemistry , Escherichia coli/chemistry , Isotope Labeling/methods , Cholesterol Oxidase/biosynthesis , Cholesterol Oxidase/genetics , Crystallography, X-Ray , Escherichia coli/enzymology , Escherichia coli/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics
14.
Naunyn Schmiedebergs Arch Pharmacol ; 388(2): 153-60, 2015 Feb.
Article in English | MEDLINE | ID: mdl-24961462

ABSTRACT

Like phosphorylation of serine, threonine, and tyrosine residues in many organisms, reversible histidine phosphorylation is a well-known regulatory signal in prokaryotes and lower eukaryotes. In vertebrates, phosphohistidine has been mainly described as a phosphorylated intermediate in enzymatic reactions, and it was believed that regulatory histidine phosphorylation is of minor importance. During the last decade, it became evident however, that nucleoside diphosphate kinase (NDPK), an ubiquitously expressed enzyme required for nucleotide homeostasis, can additionally act as a protein histidine kinase. Especially for the isoform NDPK B, at least three defined substrates, the ß subunit of heterotrimeric G proteins (Gß), the intermediate conductance potassium channel KCa3.1, and the Ca(2+)-conducting TRP channel family member, TRPV5, have been identified. In all three proteins, the phosphorylation of a specific histidine residue is of regulatory importance for protein function, and these phosphohistidines are cleaved by a counteracting 14 kDa phosphohistidine phosphatase (PHP). This article will therefore give an overview of our current knowledge on protein histidine phosphorylation in prokaryotes and lower eukaryotes and compare it with the regulatory phosphorylation and dephosphorylation of histidine residues in vertebrates by NDPK and PHP, respectively.


Subject(s)
Nucleoside-Diphosphate Kinase/metabolism , Protein Kinases/metabolism , Animals , Histidine/metabolism , Histidine Kinase , Humans , Phosphorylation
15.
Biochemistry ; 53(45): 7100-6, 2014 Nov 18.
Article in English | MEDLINE | ID: mdl-25330457

ABSTRACT

L-aspartate is a regulatory feedback inhibitor of the biotin-dependent enzyme pyruvate carboxylase in response to increased levels of tricarboxylic acid cycle intermediates. Detailed studies of L-aspartate inhibition of pyruvate carboxylase have been mainly confined to eukaryotic microbial enzymes, and aspects of its mode of action remain unclear. Here we examine its inhibition of the bacterial enzyme Rhizobium etli pyruvate carboxylase. Kinetic studies demonstrated that L-aspartate binds to the enzyme cooperatively and inhibits the enzyme competitively with respect to acetyl-CoA. L-aspartate also inhibits activation of the enzyme by MgTNP-ATP. The action of L-aspartate was not confined to inhibition of acetyl-CoA binding, because the acetyl-CoA-independent activity of the enzyme was also inhibited by increasing concentrations of L-aspartate. This inhibition of acetyl-CoA-independent activity was demonstrated to be focused in the biotin carboxylation domain of the enzyme, and it had no effect on the oxamate-induced oxaloacetate decarboxylation reaction that occurs in the carboxyl transferase domain. L-aspartate was shown to competitively inhibit bicarbonate-dependent MgATP cleavage with respect to MgATP but also probably inhibits carboxybiotin formation and/or translocation of the carboxybiotin to the site of pyruvate carboxylation. Unlike acetyl-CoA, L-aspartate has no effect on the coupling between MgATP cleavage and oxaloacetate formation. The results suggest that the three allosteric effector sites (acetyl-CoA, MgTNP-ATP, and L-aspartate) are spatially distinct but connected by a network of allosteric interactions.


Subject(s)
Aspartic Acid/pharmacology , Pyruvate Carboxylase/antagonists & inhibitors , Rhizobium etli/enzymology , Aspartic Acid/metabolism , Enzyme Inhibitors/pharmacology , Pyruvate Carboxylase/metabolism , Rhizobium etli/drug effects
16.
Biophys J ; 106(8): 1681-90, 2014 Apr 15.
Article in English | MEDLINE | ID: mdl-24739167

ABSTRACT

DmpFG is a bifunctional enzyme comprised of an aldolase subunit, DmpG, and a dehydrogenase subunit, DmpF. The aldehyde intermediate produced by the aldolase is channeled directly through a buried molecular channel in the protein structure from the aldolase to the dehydrogenase active site. In this study, we have investigated the binding of a series of progressively larger substrates to the aldolase, DmpG, using molecular dynamics. All substrates investigated are easily accommodated within the active site, binding with free energy values comparable to the physiological substrate 4-hydroxy-2-ketovalerate. Subsequently, umbrella sampling was utilized to obtain free energy surfaces for the aldehyde intermediates (which would be generated from the aldolase reaction on each of these substrates) to move through the channel to the dehydrogenase DmpF. Small substrates were channeled with limited barriers in an energetically feasible process. We show that the barriers preventing bulky intermediates such as benzaldehyde from moving through the wild-type protein can be removed by selective mutation of channel-lining residues, demonstrating the potential for tailoring this enzyme to allow its use for the synthesis of specific chemical products. Furthermore, positions of transient escape routes in this flexible channel were determined.


Subject(s)
Fructose-Bisphosphate Aldolase/metabolism , Molecular Dynamics Simulation , Oxidoreductases/metabolism , Aldehydes/chemistry , Aldehydes/metabolism , Catalytic Domain , Fructose-Bisphosphate Aldolase/chemistry , Keto Acids/chemistry , Keto Acids/metabolism , Mutation/genetics , Oxidoreductases/chemistry , Protein Multimerization , Protein Subunits/chemistry , Protein Subunits/metabolism , Substrate Specificity , Thermodynamics
17.
Biochemistry ; 53(6): 1051-8, 2014 Feb 18.
Article in English | MEDLINE | ID: mdl-24460480

ABSTRACT

His216 is a well-conserved residue in pyruvate carboxylases and, on the basis of structures of the enzyme, appears to have a role in the binding of MgATP, forming an interaction with the 3'-hydroxyl group of the ribose ring. Mutation of this residue to asparagine results in a 9-fold increase in the Km for MgATP in its steady-state cleavage in the absence of pyruvate and a 3-fold increase in the Km for MgADP in its steady-state phosphorylation by carbamoyl phosphate. However, from single-turnover experiments of MgATP cleavage, the Kd of the enzyme·MgATP complex is essentially the same in the wild-type enzyme and H216N. Direct stopped-flow measurements of nucleotide binding and release using the fluorescent analogue FTP support these observations. However, the first-order rate constant for MgATP cleavage in the single-turnover experiments in H216N is only 0.75% of that for the wild-type enzyme, and thus, the MgATP cleavage step is rate-limiting in the steady state for H216N but not for the wild-type enzyme. Close examination of the structure of the enzyme suggested that His216 may also interact with Glu218, which in turn interacts with Glu305 to form a proton relay system involved in the deprotonation of bicarbonate. Single-turnover MgATP cleavage experiments with mutations of these two residues resulted in kinetic parameters similar to those observed in H216N. We suggest that the primary role of His216 is to coordinate the binding of MgATP and the deprotonation of bicarbonate in the reaction to form the putative carboxyphosphate intermediate by participation in a proton relay system involving Glu218 and Glu305.


Subject(s)
Adenosine Triphosphate/metabolism , Histidine/chemistry , Pyruvate Carboxylase/metabolism , Adenosine Diphosphate/metabolism , Amino Acid Sequence , Asparagine/chemistry , Bicarbonates/pharmacology , Binding Sites , Carbamyl Phosphate/metabolism , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Protein Structure, Quaternary , Pyruvate Carboxylase/chemistry , Pyruvate Carboxylase/genetics , Rhizobium etli/enzymology , Ultracentrifugation
18.
Biochem Soc Trans ; 41(4): 1023-8, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23863173

ABSTRACT

It is more than 50 years since protein histidine phosphorylation was first discovered in 1962 by Boyer and co-workers; however, histidine kinases are still much less well recognized than the serine/threonine and tyrosine kinases. The best-known histidine kinases are the two-component signalling kinases that occur in bacteria, fungi and plants. The mechanisms and functions of these kinases, their cognate response regulators and associated phosphorelay proteins are becoming increasingly well understood. When genomes of higher eukaryotes began to be sequenced, it did not appear that they contained two-component histidine kinase system homologues, apart from a couple of related mitochondrial enzymes that were later shown not to function as histidine kinases. However, as a result of the burgeoning sequencing of genomes from a wide variety of eukaryotic organisms, it is clear that there are proteins that correspond to components of the two-component histidine kinase systems in higher eukaryotes and that operational two-component kinase systems are likely to occur in these organisms. There is unequivocal direct evidence that protein histidine phosphorylation does occur in mammals. So far, only nucleoside diphosphate kinases have been shown to be involved in protein histidine phosphorylation, but their mechanisms of action are not well understood. It is clear that other, yet to be identified, histidine kinases also exist in mammals and that protein histidine phosphorylation may play important roles in higher eukaryotes.


Subject(s)
Bacteria/enzymology , Protein Kinases/metabolism , Amino Acid Sequence , Histidine Kinase , Humans , Molecular Sequence Data , Phosphorylation , Protein Kinases/chemistry , Protein Kinases/isolation & purification , Sequence Homology, Amino Acid
19.
Int J Biochem Cell Biol ; 45(8): 1878-85, 2013 Aug.
Article in English | MEDLINE | ID: mdl-23742989

ABSTRACT

The bifunctional, microbial enzyme DmpFG is comprised of two subunits: the aldolase, DmpG, and the dehydrogenase, DmpF. DmpFG is of interest due to its ability to channel substrates between the two spatially distinct active sites. While the aldolase is well studied, significantly less is known about the dehydrogenase. Steady-state kinetic measurements of the reverse reaction of DmpF confirmed that the dehydrogenase uses a ping-pong mechanism, with substrate inhibition by acetyl CoA indicating that NAD(+)/NADH and CoA/acetyl CoA bind to the same site in DmpF. The Km of DmpF for exogenous acetaldehyde as a substrate was 23.7 mM, demonstrating the necessity for the channel to deliver acetaldehyde directly from the aldolase to the dehydrogenase active site. A channeling assay on the bifunctional enzyme gave an efficiency of 93% indicating that less than 10% of the toxic acetaldehyde leaks out of the channel into the bulk media, prior to reaching the dehydrogenase active site. The thermodynamic activation parameters of the reactions catalyzed by the aldolase, the dehydrogenase and the DmpFG complex were determined. The Gibb's free energy of activation for the dehydrogenase reaction was lower than that obtained for the full DmpFG reaction, in agreement with the high kcat obtained for the dehydrogenase reaction in isolation. Furthermore, although both the DmpF and DmpG reactions occur with small, favorable entropies of activation, the full DmpFG reaction occurs with a negative entropy of activation. This supports the concept of allosteric structural communication between the two enzymes to coordinate their activities.


Subject(s)
Oxidoreductases/metabolism , Protein Subunits/metabolism , Pseudomonas/enzymology , Allosteric Regulation , Biocatalysis , Enzyme Activation , Fructose-Bisphosphate Aldolase/metabolism , Keto Acids/chemistry , Keto Acids/metabolism , Kinetics , Substrate Specificity , Thermodynamics
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