1
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Niepmann M. Importance of Michaelis Constants for Cancer Cell Redox Balance and Lactate Secretion-Revisiting the Warburg Effect. Cancers (Basel) 2024; 16:2290. [PMID: 39001354 PMCID: PMC11240417 DOI: 10.3390/cancers16132290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024] Open
Abstract
Cancer cells metabolize a large fraction of glucose to lactate, even under a sufficient oxygen supply. This phenomenon-the "Warburg Effect"-is often regarded as not yet understood. Cancer cells change gene expression to increase the uptake and utilization of glucose for biosynthesis pathways and glycolysis, but they do not adequately up-regulate the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS). Thereby, an increased glycolytic flux causes an increased production of cytosolic NADH. However, since the corresponding gene expression changes are not neatly fine-tuned in the cancer cells, cytosolic NAD+ must often be regenerated by loading excess electrons onto pyruvate and secreting the resulting lactate, even under sufficient oxygen supply. Interestingly, the Michaelis constants (KM values) of the enzymes at the pyruvate junction are sufficient to explain the priorities for pyruvate utilization in cancer cells: 1. mitochondrial OXPHOS for efficient ATP production, 2. electrons that exceed OXPHOS capacity need to be disposed of and secreted as lactate, and 3. biosynthesis reactions for cancer cell growth. In other words, a number of cytosolic electrons need to take the "emergency exit" from the cell by lactate secretion to maintain the cytosolic redox balance.
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Affiliation(s)
- Michael Niepmann
- Institute of Biochemistry, Medical Faculty, Justus-Liebig-University, 35392 Giessen, Germany
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2
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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3
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Prajapati S, Rabe von Pappenheim F, Tittmann K. Frontiers in the enzymology of thiamin diphosphate-dependent enzymes. Curr Opin Struct Biol 2022; 76:102441. [PMID: 35988322 DOI: 10.1016/j.sbi.2022.102441] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
Abstract
Enzymes that use thiamin diphosphate (ThDP), the biologically active derivative of vitamin B1, as a cofactor play important roles in cellular metabolism in all domains of life. The analysis of ThDP enzymes in the past decades have provided a general framework for our understanding of enzyme catalysis of this protein family. In this review, we will discuss recent advances in the field that include the observation of "unusual" reactions and reaction intermediates that highlight the chemical versatility of the thiamin cofactor. Further topics cover the structural basis of cooperativity of ThDP enzymes, novel insights into the mechanism and structure of selected enzymes, and the discovery of "superassemblies" as reported, for example, acetohydroxy acid synthase. Finally, we summarize recent findings in the structural organisation and mode of action of 2-keto acid dehydrogenase multienzyme complexes and discuss future directions of this exciting research field.
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Affiliation(s)
- Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany; Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany; Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany; Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany.
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4
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Gokcan H, Bedoyan JK, Isayev O. Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function. J Chem Inf Model 2022; 62:3463-3475. [PMID: 35797142 DOI: 10.1021/acs.jcim.2c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyruvate dehydrogenase complex (PDC) deficiency is a major cause of primary lactic acidemia resulting in high morbidity and mortality, with limited therapeutic options. The E1 component of the mitochondrial multienzyme PDC (PDC-E1) is a symmetric dimer of heterodimers (αβ/α'β') encoded by the PDHA1 and PDHB genes, with two symmetric active sites each consisting of highly conserved phosphorylation loops A and B. PDHA1 mutations are responsible for 82-88% of cases. Greater than 85% of E1α residues with disease-causing missense mutations (DMMs) are solvent-inaccessible, with ∼30% among those involved in subunit-subunit interface contact (SSIC). We performed molecular dynamics simulations of wild-type (WT) PDC-E1 and E1 variants with E1α DMMs at R349 and W185 (residues involved in SSIC), to investigate their impact on human PDC-E1 structure. We evaluated the change in E1 structure and dynamics and examined their implications on E1 function with the specific DMMs. We found that the dynamics of phosphorylation Loop A, which is crucial for E1 biological activity, changes with DMMs that are at least about 15 Å away. Because communication is essential for PDC-E1 activity (with alternating active sites), we also investigated the possible communication network within WT PDC-E1 via centrality analysis. We observed that DMMs altered/disrupted the communication network of PDC-E1. Collectively, these results indicate allosteric effect in PDC-E1, with implications for the development of novel small-molecule therapeutics for specific recurrent E1α DMMs such as replacements of R349 responsible for ∼10% of PDC deficiency due to E1α DMMs.
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Affiliation(s)
- Hatice Gokcan
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jirair K Bedoyan
- Division of Genetic and Genomic Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania 15224, United States.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, United States
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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5
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Pavlu-Pereira H, Lousa D, Tomé CS, Florindo C, Silva MJ, de Almeida IT, Leandro P, Rivera I, Vicente JB. Structural and functional impact of clinically relevant E1α variants causing pyruvate dehydrogenase complex deficiency. Biochimie 2021; 183:78-88. [PMID: 33588022 DOI: 10.1016/j.biochi.2021.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/19/2023]
Abstract
Pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate to acetyl-coenzyme A, hinging glycolysis and the tricarboxylic acid cycle. PDC deficiency, an inborn error of metabolism, has a broad phenotypic spectrum. Symptoms range from fatal lactic acidosis or progressive neuromuscular impairment in the neonatal period, to chronic neurodegeneration. Most disease-causing mutations in PDC deficiency affect the PDHA1 gene, encoding the α subunit of the PDC-E1 component. Detailed biophysical analysis of pathogenic protein variants is a challenging approach to support the design of therapies based on improving and correcting protein structure and function. Herein, we report the characterization of clinically relevant PDC-E1α variants identified in Portuguese PDC deficient patients. These variants bear amino acid substitutions in different structural regions of PDC-E1α. The structural and functional analyses of recombinant heterotetrameric (αα'ββ') PDC-E1 variants, combined with molecular dynamics (MD) simulations, show a limited impact of the amino acid changes on the conformational stability, apart from the increased propensity for aggregation of the p.R253G variant as compared to wild-type PDC-E1. However, all variants presented a functional impairment in terms of lower residual PDC-E1 enzymatic activity and ≈3-100 × lower affinity for the thiamine pyrophosphate (TPP) cofactor, in comparison with wild-type PDC-E1. MD simulations neatly showed generally decreased stability (increased flexibility) of all variants with respect to the WT heterotetramer, particularly in the TPP binding region. These results are discussed in light of disease severity of the patients bearing such mutations and highlight the difficulty of developing chaperone-based therapies for PDC deficiency.
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Affiliation(s)
- Hana Pavlu-Pereira
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Catarina S Tomé
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cristina Florindo
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Maria João Silva
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Tavares de Almeida
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Paula Leandro
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - Isabel Rivera
- Research Institute for Medicines (iMed.ULisboa) and Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.
| | - João B Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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6
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Marsden SR, McMillan DGG, Hanefeld U. Assessing the Thiamine Diphosphate Dependent Pyruvate Dehydrogenase E1 Subunit for Carboligation Reactions with Aliphatic Ketoacids. Int J Mol Sci 2020; 21:ijms21228641. [PMID: 33207817 PMCID: PMC7696235 DOI: 10.3390/ijms21228641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 12/31/2022] Open
Abstract
The synthetic properties of the Thiamine diphosphate (ThDP)-dependent pyruvate dehydrogenase E1 subunit from Escherichia coli (EcPDH E1) was assessed for carboligation reactions with aliphatic ketoacids. Due to its role in metabolism, EcPDH E1 was previously characterised with respect to its biochemical properties, but it was never applied for synthetic purposes. Here, we show that EcPDH E1 is a promising biocatalyst for the production of chiral α-hydroxyketones. WT EcPDH E1 shows a 180-250-fold higher catalytic efficiency towards 2-oxobutyrate or pyruvate, respectively, in comparison to engineered transketolase variants from Geobacillus stearothermophilus (TKGST). Its broad active site cleft allows for the efficient conversion of both (R)- and (S)-configured α-hydroxyaldehydes, next to linear and branched aliphatic aldehydes as acceptor substrates under kinetically controlled conditions. The alternate, thermodynamically controlled self-reaction of aliphatic aldehydes was shown to be limited to low levels of conversion, which we propose to be due to their large hydration constants. Additionally, the thermodynamically controlled approach was demonstrated to suffer from a loss of stereoselectivity, which makes it unfeasible for aliphatic substrates.
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7
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The Two-Species Model of transketolase explains donor substrate-binding, inhibition and heat-activation. Sci Rep 2020; 10:4148. [PMID: 32139871 PMCID: PMC7057962 DOI: 10.1038/s41598-020-61175-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/22/2020] [Indexed: 11/23/2022] Open
Abstract
We recently characterised a low-activity form of E. coli transketolase, TKlow, which also binds the cofactor thiamine pyrophosphate (TPP) with an affinity up to two-orders of magnitude lower than the previously known high TPP-affinity and high-activity form, TKhigh, in the presence of Mg2+. We observed previously that partial oxidation was responsible for increased TKhigh activity, while low-activity TKlow was unmodified. In the present study, the fluorescence-based cofactor-binding assay was adapted to detect binding of the β-hydroxypyruvate (HPA) donor substrate to wild-type transketolase and a variant, S385Y/D469T/R520Q, that is active towards aromatic aldehydes. Transketolase HPA affinity again revealed the two distinct forms of transketolase at a TKhigh:TKlow ratio that matched those observed previously via TPP binding to each variant. The HPA dissociation constant of TKlow was comparable to the substrate-inhibition dissociation constant, KiHPA, determined previously. We provide evidence that KiHPA is a convolution of binding to the low-activity TKlow-TKlow dimer, and the TKlow subunit of the partially-active TKhigh-TKlow mixed dimer, where HPA binding to the TKlow subunit of the mixed dimer results in inhibition of the active TKhigh subunit. Heat-activation of transketolase was similarly investigated and found to convert the TKlow subunit of the mixed dimer to have TKhigh-like properties, but without oxidation.
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8
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Hepatitis C Virus Downregulates Core Subunits of Oxidative Phosphorylation, Reminiscent of the Warburg Effect in Cancer Cells. Cells 2019; 8:cells8111410. [PMID: 31717433 PMCID: PMC6912740 DOI: 10.3390/cells8111410] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 02/08/2023] Open
Abstract
Hepatitis C Virus (HCV) mainly infects liver hepatocytes and replicates its single-stranded plus strand RNA genome exclusively in the cytoplasm. Viral proteins and RNA interfere with the host cell immune response, allowing the virus to continue replication. Therefore, in about 70% of cases, the viral infection cannot be cleared by the immune system, but a chronic infection is established, often resulting in liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). Induction of cancer in the host cells can be regarded to provide further advantages for ongoing virus replication. One adaptation in cancer cells is the enhancement of cellular carbohydrate flux in glycolysis with a reduction of the activity of the citric acid cycle and aerobic oxidative phosphorylation. To this end, HCV downregulates the expression of mitochondrial oxidative phosphorylation complex core subunits quite early after infection. This so-called aerobic glycolysis is known as the “Warburg Effect” and serves to provide more anabolic metabolites upstream of the citric acid cycle, such as amino acids, pentoses and NADPH for cancer cell growth. In addition, HCV deregulates signaling pathways like those of TNF-β and MAPK by direct and indirect mechanisms, which can lead to fibrosis and HCC.
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9
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Wilkinson HC, Dalby PA. Novel insights into transketolase activation by cofactor binding identifies two native species subpopulations. Sci Rep 2019; 9:16116. [PMID: 31695144 PMCID: PMC6834573 DOI: 10.1038/s41598-019-52647-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/21/2019] [Indexed: 12/02/2022] Open
Abstract
Transketolase (TK) cofactor binding has been studied extensively over many years, yet certain mysteries remain, such as a lack of consensus on the cooperativity of thiamine pyrophosphate (TPP) binding into the two active sites, in the presence and absence of the divalent cation, Mg2+. Using a novel fluorescence-based assay, we determined directly the dissociation constants and cooperativity of TPP binding and provide the first comprehensive study over a broad range of cofactor concentrations. We confirmed the high-affinity dissociation constants and revealed a dependence of both the affinity and cooperativity of binding on [Mg2+], which explained the previous lack of consensus. A second, discrete and previously uncharacterised low-affinity TPP binding-site was also observed, and hence indicated the existence of two forms of TK with high- (TKhigh) and low-affinity (TKlow). The relative proportions of each dimer were independent of the monomer-dimer transition, as probed by analytical ultracentrifugation at various [TK]. Mass spectrometry revealed that chemical oxidation of TKlow led to the formation of TKhigh, which was 22-fold more active than TKlow. Finally, we propose a two-species model of transketolase activation that describes the interconversions between apo-/holo-TKhigh and TKlow, and the potential to significantly improve biocatalytic activity by populating only the most active form.
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Affiliation(s)
- Henry C Wilkinson
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, UK
| | - Paul A Dalby
- Department of Biochemical Engineering, University College London, London, WC1E 6BT, UK.
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10
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Dai S, Funk LM, von Pappenheim FR, Sautner V, Paulikat M, Schröder B, Uranga J, Mata RA, Tittmann K. Low-barrier hydrogen bonds in enzyme cooperativity. Nature 2019; 573:609-613. [PMID: 31534226 DOI: 10.1038/s41586-019-1581-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/12/2019] [Indexed: 11/09/2022]
Abstract
The underlying molecular mechanisms of cooperativity and allosteric regulation are well understood for many proteins, with haemoglobin and aspartate transcarbamoylase serving as prototypical examples1,2. The binding of effectors typically causes a structural transition of the protein that is propagated through signalling pathways to remote sites and involves marked changes on the tertiary and sometimes even the quaternary level1-5. However, the origin of these signals and the molecular mechanism of long-range signalling at an atomic level remain unclear5-8. The different spatial scales and timescales in signalling pathways render experimental observation challenging; in particular, the positions and movement of mobile protons cannot be visualized by current methods of structural analysis. Here we report the experimental observation of fluctuating low-barrier hydrogen bonds as switching elements in cooperativity pathways of multimeric enzymes. We have observed these low-barrier hydrogen bonds in ultra-high-resolution X-ray crystallographic structures of two multimeric enzymes, and have validated their assignment using computational calculations. Catalytic events at the active sites switch between low-barrier hydrogen bonds and ordinary hydrogen bonds in a circuit that consists of acidic side chains and water molecules, transmitting a signal through the collective repositioning of protons by behaving as an atomistic Newton's cradle. The resulting communication synchronizes catalysis in the oligomer. Our studies provide several lines of evidence and a working model for not only the existence of low-barrier hydrogen bonds in proteins, but also a connection to enzyme cooperativity. This finding suggests new principles of drug and enzyme design, in which sequences of residues can be purposefully included to enable long-range communication and thus the regulation of engineered biomolecules.
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Affiliation(s)
- Shaobo Dai
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Lisa-Marie Funk
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Fabian Rabe von Pappenheim
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Viktor Sautner
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany
| | - Mirko Paulikat
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany
| | - Benjamin Schröder
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany
| | - Jon Uranga
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, Georg-August University Göttingen, Göttingen, Germany.
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany. .,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany.
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11
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Mehrabi P, Di Pietrantonio C, Kim TH, Sljoka A, Taverner K, Ing C, Kruglyak N, Pomès R, Pai EF, Prosser RS. Substrate-Based Allosteric Regulation of a Homodimeric Enzyme. J Am Chem Soc 2019; 141:11540-11556. [PMID: 31188575 DOI: 10.1021/jacs.9b03703] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an interprotomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by nuclear magnetic resonance and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.
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Affiliation(s)
- Pedram Mehrabi
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Department for Atomically Resolved Dynamics , Max-Planck-Institute for Structure and Dynamics of Matter , Luruper Chaussee 149 , 22761 Hamburg , Germany.,Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre , Toronto , Ontario M5G 1L7 , Canada
| | - Christopher Di Pietrantonio
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada
| | - Tae Hun Kim
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada.,Program in Molecular Medicine, Research Institute, The Hospital for Sick Children , Toronto , Ontario M5G 0A4 , Canada
| | - Adnan Sljoka
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada.,CREST, Japan Science and Technology Agency (JST), Department of Informatics, School of Science and Technology , Kwansei Gakuin University , Sanda 669-1337 , Japan.,Center for Advanced Intelligence Project, RIKEN , 1-4-1 Nihombashi, Chuo-ku , Tokyo 103-0027 , Japan
| | - Keith Taverner
- Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada
| | - Christopher Ing
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children , Toronto , Ontario M5G 0A4 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Natasha Kruglyak
- Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre , Toronto , Ontario M5G 1L7 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Régis Pomès
- Program in Molecular Medicine, Research Institute, The Hospital for Sick Children , Toronto , Ontario M5G 0A4 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - Emil F Pai
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre , Toronto , Ontario M5G 1L7 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
| | - R Scott Prosser
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario M5G 1L7 , Canada.,Department of Chemistry , University of Toronto, UTM , 3359 Mississauga Road North , Mississauga , Ontario L5L 1C6 , Canada.,Department of Biochemistry , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada
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12
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Prajapati S, Haselbach D, Wittig S, Patel MS, Chari A, Schmidt C, Stark H, Tittmann K. Structural and Functional Analyses of the Human PDH Complex Suggest a "Division-of-Labor" Mechanism by Local E1 and E3 Clusters. Structure 2019; 27:1124-1136.e4. [PMID: 31130485 DOI: 10.1016/j.str.2019.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 01/17/2019] [Accepted: 04/11/2019] [Indexed: 11/27/2022]
Abstract
The pseudo-atomic structural model of human pyruvate dehydrogenase complex (PDHc) core composed of full-length E2 and E3BP components, calculated from our cryoelectron microscopy-derived density maps at 6-Å resolution, is similar to those of prokaryotic E2 structures. The spatial organization of human PDHc components as evidenced by negative-staining electron microscopy and native mass spectrometry is not homogeneous, and entails the unanticipated formation of local clusters of E1:E2 and E3BP:E3 complexes. Such uneven, clustered organization translates into specific duties for E1-E2 clusters (oxidative decarboxylation and acetyl transfer) and E3BP-E3 clusters (regeneration of reduced lipoamide) corresponding to half-reactions of the PDHc catalytic cycle. The addition of substrate coenzyme A modulates the conformational landscape of PDHc, in particular of the lipoyl domains, extending the postulated multiple random coupling mechanism. The conformational and associated chemical landscapes of PDHc are thus not determined entirely stochastically, but are restrained and channeled through an asymmetric architecture and further modulated by substrate binding.
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Affiliation(s)
- Sabin Prajapati
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany; Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - David Haselbach
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sabine Wittig
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle/Saale, Germany
| | - Mulchand S Patel
- Jacobs School of Medicine and Biomedical Sciences, Department of Biochemistry, University at Buffalo, 955 Main Street, Buffalo, NY 14203, USA
| | - Ashwin Chari
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle/Saale, Germany.
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany; Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Am Fassberg 11, 37077 Göttingen, Germany.
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13
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McDonald T, Puchowicz M, Borges K. Impairments in Oxidative Glucose Metabolism in Epilepsy and Metabolic Treatments Thereof. Front Cell Neurosci 2018; 12:274. [PMID: 30233320 PMCID: PMC6127311 DOI: 10.3389/fncel.2018.00274] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022] Open
Abstract
There is mounting evidence that oxidative glucose metabolism is impaired in epilepsy and recent work has further characterized the metabolic mechanisms involved. In healthy people eating a traditional diet, including carbohydrates, fats and protein, the major energy substrate in brain is glucose. Cytosolic glucose metabolism generates small amounts of energy, but oxidative glucose metabolism in the mitochondria generates most ATP, in addition to biosynthetic precursors in cells. Energy is crucial for the brain to signal "normally," while loss of energy can contribute to seizure generation by destabilizing membrane potentials and signaling in the chronic epileptic brain. Here we summarize the known biochemical mechanisms that contribute to the disturbance in oxidative glucose metabolism in epilepsy, including decreases in glucose transport, reduced activity of particular steps in the oxidative metabolism of glucose such as pyruvate dehydrogenase activity, and increased anaplerotic need. This knowledge justifies the use of alternative brain fuels as sources of energy, such as ketones, TCA cycle intermediates and precursors as well as even medium chain fatty acids and triheptanoin.
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Affiliation(s)
- Tanya McDonald
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Michelle Puchowicz
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Karin Borges
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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14
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Qin M, Song H, Dai X, Chan C, Chan W, Guo Z. Single‐Turnover Kinetics Reveal a Distinct Mode of Thiamine Diphosphate‐Dependent Catalysis in Vitamin K Biosynthesis. Chembiochem 2018; 19:1514-1522. [DOI: 10.1002/cbic.201800143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Mingming Qin
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Haigang Song
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Present address: Division of Structural BiologyWellcome Trust Centre of Human GenomicsUniversity of Oxford Roosevelt Drive Oxford OX3 7BN UK
| | - Xin Dai
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Chi‐Kong Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Wan Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Zhihong Guo
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
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15
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Wielgus-Kutrowska B, Grycuk T, Bzowska A. Part-of-the-sites binding and reactivity in the homooligomeric enzymes - facts and artifacts. Arch Biochem Biophys 2018; 642:31-45. [PMID: 29408402 DOI: 10.1016/j.abb.2018.01.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/13/2018] [Accepted: 01/17/2018] [Indexed: 01/18/2023]
Abstract
For a number of enzymes composed of several subunits with the same amino acid sequence, it was documented, or suggested, that binding of a ligand, or catalysis, is carried out by a single subunit. This phenomenon may be the result of a pre-existent asymmetry of subunits or a limiting case of the negative cooperativity, and is sometimes called "half-of-the-sites binding (or reactivity)" for dimers and could be called "part-of-the-sites binding (or reactivity)" for higher oligomers. In this article, we discuss molecular mechanisms that may result in "part-of-the-sites binding (and reactivity)", offer possible explanations why it may have a beneficial role in enzyme function, and point to experimental problems in documenting this behaviour. We describe some cases, for which such a mechanism was first reported and later disproved. We also give several examples of enzymes, for which this mechanism seems to be well documented, and profitable. A majority of enzymes identified in this study as half-of-the-sites binding (or reactive) use it in the flip-flop version, in which "half-of-the-sites" refers to a particular moment in time. In general, the various variants of the mechanism seems to be employed often by oligomeric enzymes for allosteric regulation to enhance the efficiency of enzymatic reactions in many key metabolic pathways.
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Affiliation(s)
- Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
| | - Tomasz Grycuk
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Department of Physics, University of Warsaw, Pasteura 5, Warsaw, 02-093, Poland.
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16
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Design and synthesis of highly selective pyruvate dehydrogenase complex E1 inhibitors as bactericides. Bioorg Med Chem 2018; 26:84-95. [DOI: 10.1016/j.bmc.2017.11.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/02/2017] [Accepted: 11/12/2017] [Indexed: 11/20/2022]
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17
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Yan Z, Maruyama A, Arakawa T, Fushinobu S, Wakagi T. Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii. Sci Rep 2016; 6:33061. [PMID: 27619895 PMCID: PMC5020499 DOI: 10.1038/srep33061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/16/2016] [Indexed: 11/22/2022] Open
Abstract
As the first three-dimensional structure of the two-subunit type 2-oxoacid:ferredoxin oxidoreductases (OFOR) from archaea, we solved the crystal structures of STK_23000/STK_22980 (StOFOR1) and STK_24350/STK_24330 (StOFOR2) from Sulfolobus tokodaii. They showed similar overall structures, consisting of two a- and b-subunit heterodimers containing thiamin pyrophosphate (TPP) cofactor and [4Fe-4S] cluster, but lack an intramolecular ferredoxin domain. Unlike other OFORs, StOFORs can utilize both pyruvate and 2-oxoglutarate, playing a key role in the central metabolism. In the structure of StOFOR2 in unreacted pyruvate complex form, carboxylate group of pyruvate is recognized by Arg344 and Thr257 from the a-subunit, which are conserved in pyruvate:ferredoxin oxidoreductase from Desulfovbrio africanus (DaPFOR). In the structure of StOFOR1 co-crystallized with 2-oxobutyrate, electron density corresponding to a 1-hydroxypropyl group (post-decarboxylation state) was observed at the thiazole ring of TPP. The binding pockets of the StOFORs surrounding the methyl or propyl group of the ligands are wider than that of DaPFOR. Mutational analyses indicated that several residues were responsible for the broad 2-oxoacid specificity of StOFORs. We also constructed a possible complex structural model by placing a Zn(2+)-containing dicluster ferredoxin of S. tokodaii into the large pocket of StOFOR2, providing insight into the electron transfer between the two redox proteins.
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Affiliation(s)
- Zhen Yan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akane Maruyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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18
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Ambrus A, Nemeria NS, Torocsik B, Tretter L, Nilsson M, Jordan F, Adam-Vizi V. Formation of reactive oxygen species by human and bacterial pyruvate and 2-oxoglutarate dehydrogenase multienzyme complexes reconstituted from recombinant components. Free Radic Biol Med 2015; 89:642-50. [PMID: 26456061 PMCID: PMC4684775 DOI: 10.1016/j.freeradbiomed.2015.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/18/2015] [Accepted: 10/03/2015] [Indexed: 01/25/2023]
Abstract
Individual recombinant components of pyruvate and 2-oxoglutarate dehydrogenase multienzyme complexes (PDHc, OGDHc) of human and Escherichia coli (E. coli) origin were expressed and purified from E. coli with optimized protocols. The four multienzyme complexes were each reconstituted under optimal conditions at different stoichiometric ratios. Binding stoichiometries for the highest catalytic efficiency were determined from the rate of NADH generation by the complexes at physiological pH. Since some of these complexes were shown to possess 'moonlighting' activities under pathological conditions often accompanied by acidosis, activities were also determined at pH 6.3. As reactive oxygen species (ROS) generation by the E3 component of hOGDHc is a pathologically relevant feature, superoxide generation by the complexes with optimal stoichiometry was measured by the acetylated cytochrome c reduction method in both the forward and the reverse catalytic directions. Various known affectors of physiological activity and ROS production, including Ca(2+), ADP, lipoylation status or pH, were investigated. The human complexes were also reconstituted with the most prevalent human pathological mutant of the E3 component, G194C and characterized; isolated human E3 with the G194C substitution was previously reported to have an enhanced ROS generating capacity. It is demonstrated that: i. PDHc, similarly to OGDHc, is able to generate ROS and this feature is displayed by both the E. coli and human complexes, ii. Reconstituted hPDHc generates ROS at a significantly higher rate as compared to hOGDHc in both the forward and the reverse reactions when ROS generation is calculated for unit mass of their common E3 component, iii. The E1 component or E1-E2 subcomplex generates significant amount of ROS only in hOGDHc; iv. Incorporation of the G194C variant of hE3, the result of a disease-causing mutation, into reconstituted hOGDHc and hPDHc indeed leads to a decreased activity of both complexes and higher ROS generation by only hOGDHc and only in its reverse reaction.
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Affiliation(s)
- Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Natalia S Nemeria
- Department of Chemistry, Rutgers, the State University, Newark, NJ 07102, USA
| | - Beata Torocsik
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Laszlo Tretter
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Mattias Nilsson
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary
| | - Frank Jordan
- Department of Chemistry, Rutgers, the State University, Newark, NJ 07102, USA
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary.
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Jordan F, Nemeria NS. Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations. Bioorg Chem 2014; 57:251-262. [PMID: 25228115 DOI: 10.1016/j.bioorg.2014.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/11/2014] [Indexed: 11/26/2022]
Abstract
Thiamin diphosphate (ThDP), the vitamin B1 coenzyme is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/carbene/C2-carbanion of the thiazolium ring and the C2α-carbanion/enamine, once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of several intermediates which are stable under acidic conditions, solid-state NMR and circular dichroism detection of the states of ionization and tautomerization of the 4'-aminopyrimidine moiety of ThDP in some of the intermediates. These methods also enabled in some cases determination of the rate-limiting step in the complex series of steps. This review is an update of a review with the same title published by the authors in 2005 in this Journal. Much progress has been made in the intervening decade in the identification of the intermediates and their application to gain additional mechanistic insight.
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Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
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20
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Patel MS, Nemeria NS, Furey W, Jordan F. The pyruvate dehydrogenase complexes: structure-based function and regulation. J Biol Chem 2014; 289:16615-23. [PMID: 24798336 DOI: 10.1074/jbc.r114.563148] [Citation(s) in RCA: 381] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The pyruvate dehydrogenase complexes (PDCs) from all known living organisms comprise three principal catalytic components for their mission: E1 and E2 generate acetyl-coenzyme A, whereas the FAD/NAD(+)-dependent E3 performs redox recycling. Here we compare bacterial (Escherichia coli) and human PDCs, as they represent the two major classes of the superfamily of 2-oxo acid dehydrogenase complexes with different assembly of, and interactions among components. The human PDC is subject to inactivation at E1 by serine phosphorylation by four kinases, an inactivation reversed by the action of two phosphatases. Progress in our understanding of these complexes important in metabolism is reviewed.
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Affiliation(s)
- Mulchand S Patel
- From the Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, the State University of New York, Buffalo, New York 14214,
| | - Natalia S Nemeria
- the Department of Chemistry, Rutgers, the State University of New Jersey, Newark, New Jersey 07102
| | - William Furey
- the Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, and the Veterans Affairs Medical Center, Pittsburgh, Pennsylvania 15240
| | - Frank Jordan
- the Department of Chemistry, Rutgers, the State University of New Jersey, Newark, New Jersey 07102,
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21
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Jordan F, Patel H. Catalysis in Enzymatic Decarboxylations: Comparison of Selected Cofactor-dependent and Cofactor-independent Examples. ACS Catal 2013; 3:1601-1617. [PMID: 23914308 DOI: 10.1021/cs400272x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This review is focused on three types of enzymes decarboxylating very different substrates: (1) Thiamin diphosphate (ThDP)-dependent enzymes reacting with 2-oxo acids; (2) Pyridoxal phosphate (PLP)-dependent enzymes reacting with α-amino acids; and (3) An enzyme with no known co-factors, orotidine 5'-monophosphate decarboxylase (OMPDC). While the first two classes have been much studied for many years, during the past decade studies of both classes have revealed novel mechanistic insight challenging accepted understanding. The enzyme OMPDC has posed a challenge to the enzymologist attempting to explain a 1017-fold rate acceleration in the absence of cofactors or even metal ions. A comparison of the available evidence on the three types of decarboxylases underlines some common features and more differences. The field of decarboxylases remains an interesting and challenging one for the mechanistic enzymologist notwithstanding the large amount of information already available.
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Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, 73 Warren Street, Newark,
New Jersey 07102, United States
| | - Hetalben Patel
- Department of Chemistry, Rutgers, The State University of New Jersey, 73 Warren Street, Newark,
New Jersey 07102, United States
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22
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Schröder-Tittmann K, Meyer D, Arens J, Wechsler C, Tietzel M, Golbik R, Tittmann K. Alternating Sites Reactivity Is a Common Feature of Thiamin Diphosphate-Dependent Enzymes As Evidenced by Isothermal Titration Calorimetry Studies of Substrate Binding. Biochemistry 2013; 52:2505-7. [DOI: 10.1021/bi301591e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathrin Schröder-Tittmann
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Danilo Meyer
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Johannes Arens
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Cindy Wechsler
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Michael Tietzel
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
| | - Ralph Golbik
- Martin-Luther University Halle-Wittenberg, 06120 Halle/Salle, Germany
| | - Kai Tittmann
- Göttingen Center for
Molecular Biosciences, Georg-August-University Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen,
Germany
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23
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Balakrishnan A, Nemeria NS, Chakraborty S, Kakalis L, Jordan F. Determination of pre-steady-state rate constants on the Escherichia coli pyruvate dehydrogenase complex reveals that loop movement controls the rate-limiting step. J Am Chem Soc 2012; 134:18644-55. [PMID: 23088422 DOI: 10.1021/ja3062375] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Spectroscopic identification and characterization of covalent and noncovalent intermediates on large enzyme complexes is an exciting and challenging area of modern enzymology. The Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), consisting of multiple copies of enzymic components and coenzymes, performs the oxidative decarboxylation of pyruvate to acetyl-CoA and is central to carbon metabolism linking glycolysis to the Krebs cycle. On the basis of earlier studies, we hypothesized that the dynamic regions of the E1p component, which undergo a disorder-order transition upon substrate binding to thiamin diphosphate (ThDP), play a critical role in modulation of the catalytic cycle of PDHc. To test our hypothesis, we kinetically characterized ThDP-bound covalent intermediates on the E1p component, and the lipoamide-bound covalent intermediate on the E2p component in PDHc and in its variants with disrupted active-site loops. Our results suggest that formation of the first covalent predecarboxylation intermediate, C2α-lactylthiamin diphosphate (LThDP), is rate limiting for the series of steps culminating in acetyl-CoA formation. Substitutions in the active center loops produced variants with up to 900-fold lower rates of formation of the LThDP, demonstrating that these perturbations directly affected covalent catalysis. This rate was rescued by up to 5-fold upon assembly to PDHc of the E401K variant. The E1p loop dynamics control covalent catalysis with ThDP and are modulated by PDHc assembly, presumably by selection of catalytically competent loop conformations. This mechanism could be a general feature of 2-oxoacid dehydrogenase complexes because such interfacial dynamic regions are highly conserved.
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Affiliation(s)
- Anand Balakrishnan
- Department of Chemistry, Rutgers the State University, Newark, New Jersey 07102, United States
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24
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Neves A, Costalat R, Pellerin L. Determinants of brain cell metabolic phenotypes and energy substrate utilization unraveled with a modeling approach. PLoS Comput Biol 2012; 8:e1002686. [PMID: 23028284 PMCID: PMC3441424 DOI: 10.1371/journal.pcbi.1002686] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/23/2012] [Indexed: 12/31/2022] Open
Abstract
Although all brain cells bear in principle a comparable potential in terms of energetics, in reality they exhibit different metabolic profiles. The specific biochemical characteristics explaining such disparities and their relative importance are largely unknown. Using a modeling approach, we show that modifying the kinetic parameters of pyruvate dehydrogenase and mitochondrial NADH shuttling within a realistic interval can yield a striking switch in lactate flux direction. In this context, cells having essentially an oxidative profile exhibit pronounced extracellular lactate uptake and consumption. However, they can be turned into cells with prominent aerobic glycolysis by selectively reducing the aforementioned parameters. In the case of primarily oxidative cells, we also examined the role of glycolysis and lactate transport in providing pyruvate to mitochondria in order to sustain oxidative phosphorylation. The results show that changes in lactate transport capacity and extracellular lactate concentration within the range described experimentally can sustain enhanced oxidative metabolism upon activation. Such a demonstration provides key elements to understand why certain brain cell types constitutively adopt a particular metabolic profile and how specific features can be altered under different physiological and pathological conditions in order to face evolving energy demands. In an environment with appropriate oxygen levels (normoxia), most eukaryotic cells produce energy by oxidizing glucose into carbon dioxide and water. In this process, glucose is transformed into pyruvate, which then fuels oxidative phosphorylation in the mitochondria. Interestingly, Otto Warburg reported back in the 1920's that some eukaryotic cells prominently process glucose-derived pyruvate into lactate, hence “avoiding" the mitochondrial oxidation despite adequate oxygen concentrations. This phenomenon was termed aerobic glycolysis and was first observed in cancer cells. Since then, it has also been described in several normal tissues including the central nervous system. The biochemical basis of aerobic glycolysis has remained elusive until now. Taking advantage of a modeling approach, we unraveled the main metabolic characteristics that determine whether a cell will be strictly oxidative or rather will exhibit aerobic glycolysis. When applied in the context of the central nervous system, our findings not only provide a theoretical demonstration of why neurons and astrocytes differ in terms of metabolic profile, but also suggest that such complementarity forms the basis for metabolic cooperation between the two cell types.
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Affiliation(s)
- Aitana Neves
- Département de Physiologie, Université de Lausanne, Lausanne, Switzerland
| | | | - Luc Pellerin
- Département de Physiologie, Université de Lausanne, Lausanne, Switzerland
- * E-mail:
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25
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Novak BR, Moldovan D, Waldrop GL, de Queiroz MS. Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations. Proteins 2011; 79:622-32. [PMID: 21120858 DOI: 10.1002/prot.22910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ∼45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg(2)ATP, a monomer with bound Mg(2)ATP, and a homodimer with bound Mg(2)ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg(2)ATP. For the dimer with Mg(2)ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg(2)ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg(2)ATP is only approximately 2k(B)T higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg(2)ATP are much smaller than the overall reaction time, which is on the order of seconds.
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Affiliation(s)
- Brian R Novak
- Department of Mechanical Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
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26
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Brovetto M, Gamenara D, Méndez PS, Seoane GA. C-C bond-forming lyases in organic synthesis. Chem Rev 2011; 111:4346-403. [PMID: 21417217 DOI: 10.1021/cr100299p] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Margarita Brovetto
- Grupo de Fisicoquímica Orgánica y Bioprocesos, Departamento de Química Orgánica, DETEMA, Facultad de Química, Universidad de la República (UdelaR), Gral. Flores 2124, 11800 Montevideo, Uruguay
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27
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Steinmetz A, Vyazmensky M, Meyer D, Barak Z, Golbik R, Chipman DM, Tittmann K. Valine 375 and Phenylalanine 109 Confer Affinity and Specificity for Pyruvate as Donor Substrate in Acetohydroxy Acid Synthase Isozyme II from Escherichia coli. Biochemistry 2010; 49:5188-99. [DOI: 10.1021/bi100555q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Steinmetz
- Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Maria Vyazmensky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Danilo Meyer
- Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Ze′ev Barak
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ralph Golbik
- Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - David M. Chipman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Kai Tittmann
- Albrecht-von-Haller-Institute and Göttingen Centre for Molecular Biosciences, Ernst-Caspari-Haus, Department of Bioanalytics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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28
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Isaev AN. Quantum-chemical calculations of a long proton wire. Application of a harmonic model to analysis of the structure of an ionic defect in a water chain with an excess proton. J Phys Chem A 2010; 114:2201-12. [PMID: 20085360 DOI: 10.1021/jp908259p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum-chemical calculations of molecular complexes (NH(3))(3)Zn(2+)...(H(2)O)(n)...NH(3) (C(n), n = 11, 16, 21, and 30) simulating a proton wire donor-water chain-acceptor were carried out. Earlier found periodicity in the length of the O-H bonds in water chain is explained within the framework of a one-component harmonic model. In complexes C(n), the geometry and electronic structure of ionic defect in water chain with an excess proton were studied. Calculations carried out at ab initio (B3LYP/6-31+G**) and semiempirical (PM3) levels of theory predict different patterns of distribution of the O-H bonds lengths and positive charge on the H-bond hydrogen atoms in the region of ionic defect. The obtained data show how a length of water chain and position of a protonated water link in the chain influence the ionic defect structure. To describe the observed structures of ionic defect, the harmonic model was used and the role of parameters of the H-bonded chain was investigated. The performed analysis explains different mechanisms (concerted and stepwise) of proton transfer along the H-bonded chain derived from ab initio and semiempirical calculation schemes.
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Affiliation(s)
- Alexander N Isaev
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky pr. 47, 119991 Moscow, Russia.
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29
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Nemeria NS, Arjunan P, Chandrasekhar K, Mossad M, Tittmann K, Furey W, Jordan F. Communication between thiamin cofactors in the Escherichia coli pyruvate dehydrogenase complex E1 component active centers: evidence for a "direct pathway" between the 4'-aminopyrimidine N1' atoms. J Biol Chem 2010; 285:11197-209. [PMID: 20106967 DOI: 10.1074/jbc.m109.069179] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinetic, spectroscopic, and structural analysis tested the hypothesis that a chain of residues connecting the 4'-aminopyrimidine N1' atoms of thiamin diphosphates (ThDPs) in the two active centers of the Escherichia coli pyruvate dehydrogenase complex E1 component provides a signal transduction pathway. Substitution of the three acidic residues (Glu(571), Glu(235), and Glu(237)) and Arg(606) resulted in impaired binding of the second ThDP, once the first active center was filled, suggesting a pathway for communication between the two ThDPs. 1) Steady-state kinetic and fluorescence quenching studies revealed that upon E571A, E235A, E237A, and R606A substitutions, ThDP binding in the second active center was affected. 2) Analysis of the kinetics of thiazolium C2 hydrogen/deuterium exchange of enzyme-bound ThDP suggests half-of-the-sites reactivity for the E1 component, with fast (activated site) and slow exchanging sites (dormant site). The E235A and E571A variants gave no evidence for the slow exchanging site, indicating that only one of two active sites is filled with ThDP. 3) Titration of the E235A and E237A variants with methyl acetylphosphonate monitored by circular dichroism suggested that only half of the active sites were filled with a covalent predecarboxylation intermediate analog. 4) Crystal structures of E235A and E571A in complex with ThDP revealed the structural basis for the spectroscopic and kinetic observations and showed that either substitution affects cofactor binding, despite the fact that Glu(235) makes no direct contact with the cofactor. The role of the conserved Glu(571) residue in both catalysis and cofactor orientation is revealed by the combined results for the first time.
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Affiliation(s)
- Natalia S Nemeria
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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30
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X-ray crystallographic snapshots of reaction intermediates in pyruvate oxidase and transketolase illustrate common themes in thiamin catalysis. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Kale S, Jordan F. Conformational ensemble modulates cooperativity in the rate-determining catalytic step in the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex. J Biol Chem 2009; 284:33122-9. [PMID: 19801660 DOI: 10.1074/jbc.m109.065508] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cooperativity is extensively used by enzymes, particularly those acting at key metabolic branch points, to "fine tune" catalysis. Thus, cooperativity and enzyme catalysis are intimately linked, yet their linkage is poorly understood. Here we show that negative cooperativity in the rate-determining step in the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex is an outcome of redistribution of a "rate-promoting" conformational pre-equilibrium. An array of biophysical and biochemical studies indicates that non-catalytic but conserved residues directly regulate the redistribution. Furthermore, factors such as ligands and temperature, individually or in concert, also strongly influence the redistribution. As a consequence, these factors also exert their influence on catalysis by profoundly influencing the pre-equilibrium facilitated dynamics of communication between multienzyme components. Our observations suggest a mode of cooperativity in the E1 component that is consistent with the dynamical hypothesis shown to satisfactorily explain cooperativity in many well studied enzymes. The results point to the likely existence of multiple modes of communication between subunits when the entire class of thiamin diphosphate-dependent enzymes is considered.
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Affiliation(s)
- Sachin Kale
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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32
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Brandt GS, Kneen MM, Chakraborty S, Baykal AT, Nemeria N, Yep A, Ruby DI, Petsko GA, Kenyon GL, McLeish MJ, Jordan F, Ringe D. Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor. Biochemistry 2009; 48:3247-57. [PMID: 19320438 DOI: 10.1021/bi801950k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral alpha-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2alpha-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2alpha-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 A (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.
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Affiliation(s)
- Gabriel S Brandt
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA
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33
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Nemeria NS, Chakraborty S, Balakrishnan A, Jordan F. Reaction mechanisms of thiamin diphosphate enzymes: defining states of ionization and tautomerization of the cofactor at individual steps. FEBS J 2009; 276:2432-46. [PMID: 19476485 DOI: 10.1111/j.1742-4658.2009.06964.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We summarize the currently available information regarding the state of ionization and tautomerization of the 4'-aminopyrimidine ring of the thiamine diphosphate on enzymes requiring this coenzyme. This coenzyme forms a series of covalent intermediates with its substrates as an electrophilic catalyst, and the coenzyme itself also carries out intramolecular proton transfers, which is virtually unprecedented in coenzyme chemistry. An understanding of the state of ionization and tautomerization of the 4'-aminopyrimidine ring in each of these intermediates provides important details about proton movements during catalysis. CD spectroscopy, both steady-state and time-resolved, has proved crucial for obtaining this information because no other experimental method has provided such atomic detail so far.
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Affiliation(s)
- Natalia S Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ, USA.
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34
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Kato M, Wynn RM, Chuang JL, Tso SC, Machius M, Li J, Chuang DT. Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops. Structure 2009; 16:1849-59. [PMID: 19081061 DOI: 10.1016/j.str.2008.10.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 10/26/2008] [Accepted: 10/27/2008] [Indexed: 11/15/2022]
Abstract
We report the crystal structures of the phosporylated pyruvate dehydrogenase (E1p) component of the human pyruvate dehydrogenase complex (PDC). The complete phosphorylation at Ser264-alpha (site 1) of a variant E1p protein was achieved using robust pyruvate dehydrogenase kinase 4 free of the PDC core. We show that unlike its unmodified counterpart, the presence of a phosphoryl group at Ser264-alpha prevents the cofactor thiamine diphosphate-induced ordering of the two loops carrying the three phosphorylation sites. The disordering of these phosphorylation loops is caused by a previously unrecognized steric clash between the phosphoryl group at site 1 and a nearby Ser266-alpha, which nullifies a hydrogen-bonding network essential for maintaining the loop conformations. The disordered phosphorylation loops impede the binding of lipoyl domains of the PDC core to E1p, negating the reductive acetylation step. This results in the disruption of the substrate channeling in the PDC, leading to the inactivation of this catalytic machine.
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Affiliation(s)
- Masato Kato
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9038, USA
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35
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Pei XY, Titman CM, Frank RA, Leeper FJ, Luisi BF. Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multienzyme complex. Structure 2008; 16:1860-72. [PMID: 19081062 PMCID: PMC2663715 DOI: 10.1016/j.str.2008.10.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 09/10/2008] [Accepted: 10/01/2008] [Indexed: 11/15/2022]
Abstract
The pyruvate dehydrogenase multienzyme assembly (PDH) generates acetyl coenzyme A and reducing equivalents from pyruvate in a multiple-step process that is a nexus of central metabolism. We report crystal structures of the Geobacillus stearothermophilus PDH E1p subunit with ligands that mimic the prereaction complex and the postdecarboxylation product. The structures implicate residues that help to orient substrates, nurture intermediates, and organize surface loops so that they can engage a mobile lipoyl domain that receives the acetyl group and shuttles it to the next active site. The structural and enzymatic data suggest that H128beta performs a dual role: first, as electrostatic catalyst of the reaction of pyruvate with the thiamine cofactor; and second, as a proton donor in the second reaction of acetyl group with the lipoate. We also identify I206alpha as a key residue in mediating the conformation of active-site loops. We propose that a simple conformational flip of the H271alpha side chain assists transfer of the acetyl group from thiamine cofactor to lipoyl domain in synchrony with reduction of the dithiolane ring.
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Affiliation(s)
- Xue Yuan Pei
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Christopher M. Titman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - René A.W. Frank
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Finian J. Leeper
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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36
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Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli. Proc Natl Acad Sci U S A 2008; 105:17390-5. [PMID: 18988747 DOI: 10.1073/pnas.0805027105] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The thiamin- and flavin-dependent peripheral membrane enzyme pyruvate oxidase from E. coli catalyzes the oxidative decarboxylation of the central metabolite pyruvate to CO(2) and acetate. Concomitant reduction of the enzyme-bound flavin triggers membrane binding of the C terminus and shuttling of 2 electrons to ubiquinone 8, a membrane-bound mobile carrier of the electron transport chain. Binding to the membrane in vivo or limited proteolysis in vitro stimulate the catalytic proficiency by 2 orders of magnitude. The molecular mechanisms by which membrane binding and activation are governed have remained enigmatic. Here, we present the X-ray crystal structures of the full-length enzyme and a proteolytically activated truncation variant lacking the last 23 C-terminal residues inferred as important in membrane binding. In conjunction with spectroscopic results, the structural data pinpoint a conformational rearrangement upon activation that exposes the autoinhibitory C terminus, thereby freeing the active site. In the activated enzyme, Phe-465 swings into the active site and wires both cofactors for efficient electron transfer. The isolated C terminus, which has no intrinsic helix propensity, folds into a helical structure in the presence of micelles.
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37
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Mochalkin I, Miller JR, Evdokimov A, Lightle S, Yan C, Stover CK, Waldrop GL. Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase. Protein Sci 2008; 17:1706-18. [PMID: 18725455 PMCID: PMC2548373 DOI: 10.1110/ps.035584.108] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Bacterial acetyl-CoA carboxylase is a multifunctional biotin-dependent enzyme that consists of three separate proteins: biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and carboxyltransferase (CT). Acetyl-CoA carboxylase is a potentially attractive target for novel antibiotics because it catalyzes the first committed step in fatty acid biosynthesis. In the first half-reaction, BC catalyzes the ATP-dependent carboxylation of BCCP. In the second half-reaction, the carboxyl group is transferred from carboxybiotinylated BCCP to acetyl-CoA to produce malonyl-CoA. A series of structures of BC from several bacteria crystallized in the presence of various ATP analogs is described that addresses three major questions concerning the catalytic mechanism. The structure of BC bound to AMPPNP and the two catalytically essential magnesium ions resolves inconsistencies between the kinetics of active-site BC mutants and previously reported BC structures. Another structure of AMPPNP bound to BC shows the polyphosphate chain folded back on itself, and not in the correct (i.e., extended) conformation for catalysis. This provides the first structural evidence for the hypothesis of substrate-induced synergism, which posits that ATP binds nonproductively to BC in the absence of biotin. The BC homodimer has been proposed to exhibit half-sites reactivity where the active sites alternate or "flip-flop" their catalytic cycles. A crystal structure of BC showed the ATP analog AMPPCF(2)P bound to one subunit while the other subunit was unliganded. The liganded subunit was in the closed or catalytic conformation while the unliganded subunit was in the open conformation. This provides the first structural evidence for half-sites reactivity in BC.
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Affiliation(s)
- Igor Mochalkin
- Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA
| | - J. Richard Miller
- Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA
| | - Artem Evdokimov
- Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA
| | - Sandra Lightle
- Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA
| | - Chunhong Yan
- Pfizer Global Research and Development, Ann Arbor, Michigan 48105, USA
| | | | - Grover L. Waldrop
- Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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38
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Kluger R, Tittmann K. Thiamin diphosphate catalysis: enzymic and nonenzymic covalent intermediates. Chem Rev 2008; 108:1797-833. [PMID: 18491870 DOI: 10.1021/cr068444m] [Citation(s) in RCA: 195] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ronald Kluger
- Davenport Laboratories, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada.
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39
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Lengyel JS, Stott KM, Wu X, Brooks BR, Balbo A, Schuck P, Perham RN, Subramaniam S, Milne JLS. Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex. Structure 2008; 16:93-103. [PMID: 18184587 DOI: 10.1016/j.str.2007.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 10/15/2007] [Accepted: 10/17/2007] [Indexed: 10/22/2022]
Abstract
Icosahedral pyruvate dehydrogenase (PDH) enzyme complexes are molecular machines consisting of a central E2 core decorated by a shell of peripheral enzymes (E1 and E3) found localized at a distance of approximately 75-90 A from the core. Using a combination of biochemical, biophysical, and cryo-electron microscopic techniques, we show here that the gap between the E2 core and the shell of peripheral enzymes is maintained by the flexible but extended conformation adopted by 60 linker polypeptides that radiate outwards from the inner E2 core, irrespective of the E1 or E3 occupancy. The constancy of the gap is thus not due to protein-protein interactions in the outer protein shell. The extended nature of the E2 inner-linker regions thereby creates the restricted annular space in which the lipoyl domains of E2 that carry catalytic intermediates shuttle between E1, E2, and E3 active sites, while their conformational flexibility facilitates productive encounters.
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Affiliation(s)
- Jeffrey S Lengyel
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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40
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Versées W, Spaepen S, Vanderleyden J, Steyaert J. The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 Å resolution. FEBS J 2007; 274:2363-75. [PMID: 17403037 DOI: 10.1111/j.1742-4658.2007.05771.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenylpyruvate decarboxylase (PPDC) of Azospirillum brasilense, involved in the biosynthesis of the plant hormone indole-3-acetic acid and the antimicrobial compound phenylacetic acid, is a thiamine diphosphate-dependent enzyme that catalyses the nonoxidative decarboxylation of indole- and phenylpyruvate. Analogous to yeast pyruvate decarboxylases, PPDC is subject to allosteric substrate activation, showing sigmoidal v versus [S] plots. The present paper reports the crystal structure of this enzyme determined at 1.5 A resolution. The subunit architecture of PPDC is characteristic for other members of the pyruvate oxidase family, with each subunit consisting of three domains with an open alpha/beta topology. An active site loop, bearing the catalytic residues His112 and His113, could not be modelled due to flexibility. The biological tetramer is best described as an asymmetric dimer of dimers. A cysteine residue that has been suggested as the site for regulatory substrate binding in yeast pyruvate decarboxylase is not conserved, requiring a different mechanism for allosteric substrate activation in PPDC. Only minor changes occur in the interactions with the cofactors, thiamine diphosphate and Mg2+, compared to pyruvate decarboxylase. A greater diversity is observed in the substrate binding pocket accounting for the difference in substrate specificity. Moreover, a catalytically important glutamate residue conserved in nearly all decarboxylases is replaced by a leucine in PPDC. The consequences of these differences in terms of the catalytic and regulatory mechanism of PPDC are discussed.
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Affiliation(s)
- Wim Versées
- Department of Ultrastructure, Vrije Universiteit Brussel, Brussels, Belgium.
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41
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Li J, Machius M, Chuang JL, Wynn RM, Chuang DT. The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism. J Biol Chem 2007; 282:11904-13. [PMID: 17329260 DOI: 10.1074/jbc.m610843200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A long standing controversy is whether an alternating activesite mechanism occurs during catalysis in thiamine diphosphate (ThDP)-dependent enzymes. We address this question by investigating the ThDP-dependent decarboxylase/dehydrogenase (E1b) component of the mitochondrial branched-chain alpha-keto acid dehydrogenase complex (BCKDC). Our crystal structure reveals that conformations of the two active sites in the human E1b heterotetramer harboring the reaction intermediate are identical. Acidic residues in the core of the E1b heterotetramer, which align with the proton-wire residues proposed to participate in active-site communication in the related pyruvate dehydrogenase from Bacillus stearothermophilus, are mutated. Enzyme kinetic data show that, except in a few cases because of protein misfolding, these alterations are largely without effect on overall activity of BCKDC, ruling out the requirement of a proton-relay mechanism in E1b. BCKDC overall activity is nullified at 50% phosphorylation of E1b, but it is restored to nearly half of the pre-phosphorylation level after dissociation and reconstitution of BCKDC with the same phosphorylated E1b. The results suggest that the abolition of overall activity likely results from the specific geometry of the half-phosphorylated E1b in the BCKDC assembly and not due to a disruption of the alternating active-site mechanism. Finally, we show that a mutant E1b containing only one functional active site exhibits half of the wild-type BCKDC activity, which directly argues against the obligatory communication between active sites. The above results provide evidence that the two active sites in the E1b heterotetramer operate independently during the ThDP-dependent decarboxylation reaction.
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Affiliation(s)
- Jun Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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42
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Islam MM, Wallin R, Wynn RM, Conway M, Fujii H, Mobley JA, Chuang DT, Hutson SM. A novel branched-chain amino acid metabolon. Protein-protein interactions in a supramolecular complex. J Biol Chem 2007; 282:11893-903. [PMID: 17314104 DOI: 10.1074/jbc.m700198200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The catabolic pathways of branched-chain amino acids have two common steps. The first step is deamination catalyzed by the vitamin B(6)-dependent branched-chain aminotransferase isozymes (BCATs) to produce branched-chain alpha-keto acids (BCKAs). The second step is oxidative decarboxylation of the BCKAs mediated by the branched-chain alpha-keto acid dehydrogenase enzyme complex (BCKD complex). The BCKD complex is organized around a cubic core consisting of 24 lipoate-bearing dihydrolipoyl transacylase (E2) subunits, associated with the branched-chain alpha-keto acid decarboxylase/dehydrogenase (E1), dihydrolipoamide dehydrogenase (E3), BCKD kinase, and BCKD phosphatase. In this study, we provide evidence that human mitochondrial BCAT (hBCATm) associates with the E1 decarboxylase component of the rat or human BCKD complex with a K(D) of 2.8 microM. NADH dissociates the complex. The E2 and E3 components do not interact with hBCATm. In the presence of hBCATm, k(cat) values for E1-catalyzed decarboxylation of the BCKAs are enhanced 12-fold. Mutations of hBCATm proteins in the catalytically important CXXC center or E1 proteins in the phosphorylation loop residues prevent complex formation, indicating that these regions are important for the interaction between hBCATm and E1. Our results provide evidence for substrate channeling between hBCATm and BCKD complex and formation of a metabolic unit (termed branched-chain amino acid metabolon) that can be influenced by the redox state in mitochondria.
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Affiliation(s)
- Mohammad Mainul Islam
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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43
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Nemeria N, Chakraborty S, Baykal A, Korotchkina LG, Patel MS, Jordan F. The 1',4'-iminopyrimidine tautomer of thiamin diphosphate is poised for catalysis in asymmetric active centers on enzymes. Proc Natl Acad Sci U S A 2007; 104:78-82. [PMID: 17182735 PMCID: PMC1765481 DOI: 10.1073/pnas.0609973104] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Indexed: 11/18/2022] Open
Abstract
Thiamin diphosphate, a key coenzyme in sugar metabolism, is comprised of the thiazolium and 4'-aminopyrimidine aromatic rings, but only recently has participation of the 4'-aminopyrimidine moiety in catalysis gained wider acceptance. We report the use of electronic spectroscopy to identify the various tautomeric forms of the 4'-aminopyrimidine ring on four thiamin diphosphate enzymes, all of which decarboxylate pyruvate: the E1 component of human pyruvate dehydrogenase complex, the E1 subunit of Escherichia coli pyruvate dehydrogenase complex, yeast pyruvate decarboxylase, and pyruvate oxidase from Lactobacillus plantarum. It is shown that, according to circular dichroism spectroscopy, both the 1',4'-iminopyrimidine and the 4'-aminopyrimidine tautomers coexist on the E1 component of human pyruvate dehydrogenase complex and pyruvate oxidase. Because both tautomers are seen simultaneously, these two enzymes provide excellent evidence for nonidentical active centers (asymmetry) in solution in these multimeric enzymes. Asymmetry of active centers can also be induced upon addition of acetylphosphinate, an excellent electrostatic pyruvate mimic, which participates in an enzyme-catalyzed addition to form a stable adduct, resembling the common predecarboxylation thiamin-bound intermediate, which exists in its 1',4'-iminopyrimidine form. The identification of the 1',4'-iminopyrimidine tautomer on four enzymes is almost certainly applicable to all thiamin diphosphate enzymes: this tautomer is the intramolecular trigger to generate the reactive ylide/carbene at the thiazolium C2 position in the first fundamental step of thiamin catalysis.
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Affiliation(s)
- Natalia Nemeria
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102; and
| | - Sumit Chakraborty
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102; and
| | - Ahmet Baykal
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102; and
| | - Lioubov G. Korotchkina
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14214
| | - Mulchand S. Patel
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14214
| | - Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, Newark, NJ 07102; and
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Jordan F, Nemeria NS. Experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations. Bioorg Chem 2005; 33:190-215. [PMID: 15888311 PMCID: PMC4189838 DOI: 10.1016/j.bioorg.2005.02.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 02/08/2005] [Accepted: 02/10/2005] [Indexed: 11/27/2022]
Abstract
Thiamin diphosphate (ThDP), the vitamin B1 coenzyme, is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/C2-carbanion of the thiazolium ring and the C2alpha-carbanion (or enamine) once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state (X-ray) methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of a several intermediates which are stable under acidic conditions, and circular dichroism detection of the 1',4'-imino tautomer of ThDP in some of the intermediates. Some of these methods also enable the investigator to determine the rate-limiting step in the complex series of steps.
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Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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