1
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Toci EM, Austin SL, Majumdar A, Woodcock HL, Freel Meyers CL. Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1-Deoxy-d-xylulose-5-phosphate Synthase. Biochemistry 2024; 63:671-687. [PMID: 38393327 PMCID: PMC11015862 DOI: 10.1021/acs.biochem.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The bacterial metabolic enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde-3-phosphate (d-GAP). DXP is an essential bacteria-specific metabolite that feeds into the biosynthesis of isoprenoids, pyridoxal phosphate (PLP), and ThDP. DXPS catalyzes the activation of pyruvate to give the C2α-lactylThDP (LThDP) adduct that is long-lived on DXPS in a closed state in the absence of the cosubstrate. Binding of d-GAP shifts the DXPS-LThDP complex to an open state which coincides with LThDP decarboxylation. This gated mechanism distinguishes DXPS in ThDP enzymology. How LThDP persists on DXPS in the absence of cosubstrate, while other pyruvate decarboxylases readily activate LThDP for decarboxylation, is a long-standing question in the field. We propose that an active site network functions to prevent LThDP activation on DXPS until the cosubstrate binds. Binding of d-GAP coincides with a conformational shift and disrupts the network causing changes in the active site that promote LThDP activation. Here, we show that the substitution of putative network residues, as well as nearby residues believed to contribute to network charge distribution, predictably affects LThDP reactivity. Substitutions predicted to disrupt the network have the effect to activate LThDP for decarboxylation, resulting in CO2 and acetate production. In contrast, a substitution predicted to strengthen the network fails to activate LThDP and has the effect to shift DXPS toward the closed state. Network-disrupting substitutions near the carboxylate of LThDP also have a pronounced effect to shift DXPS to an open state. These results offer initial insights to explain the long-lived LThDP intermediate and its activation through disruption of an active site network, which is unique to DXPS. These findings have important implications for DXPS function in bacteria and its development as an antibacterial target.
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Affiliation(s)
- Eucolona M Toci
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Ananya Majumdar
- Biomolecular NMR Center, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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2
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Moxley WC, Brown RE, Eiteman MA. Escherichia coli aceE variants coding pyruvate dehydrogenase improve the generation of pyruvate-derived acetoin. Eng Life Sci 2023; 23:e2200054. [PMID: 36874610 PMCID: PMC9978916 DOI: 10.1002/elsc.202200054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/23/2022] [Accepted: 01/07/2023] [Indexed: 02/04/2023] Open
Abstract
Several chromosomally expressed AceE variants were constructed in Escherichia coli ΔldhA ΔpoxB ΔppsA and compared using glucose as the sole carbon source. These variants were examined in shake flask cultures for growth rate, pyruvate accumulation, and acetoin production via heterologous expression of the budA and budB genes from Enterobacter cloacae ssp. dissolvens. The best acetoin-producing strains were subsequently studied in controlled batch culture at the one-liter scale. PDH variant strains attained up to four-fold greater acetoin than the strain expressing the wild-type PDH. In a repeated batch process, the H106V PDH variant strain attained over 43 g/L of pyruvate-derived products, acetoin (38.5 g/L) and 2R,3R-butanediol (5.0 g/L), corresponding to an effective concentration of 59 g/L considering the dilution. The acetoin yield from glucose was 0.29 g/g with a volumetric productivity of 0.9 g/L·h (0.34 g/g and 1.0 g/L·h total products). The results demonstrate a new tool in pathway engineering, the modification of a key metabolic enzyme to improve the formation of a product via a kinetically slow, introduced pathway. Direct modification of the pathway enzyme offers an alternative to promoter engineering in cases where the promoter is involved in a complex regulatory network.
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Affiliation(s)
- W Chris Moxley
- Department of Microbiology University of Georgia Athens Georgia USA
| | - Rachel E Brown
- School of Chemical Materials and Biomedical Engineering University of Georgia Athens Georgia USA
| | - Mark A Eiteman
- Department of Microbiology University of Georgia Athens Georgia USA.,School of Chemical Materials and Biomedical Engineering University of Georgia Athens Georgia USA
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3
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Škerlová J, Berndtsson J, Nolte H, Ott M, Stenmark P. Structure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion. Nat Commun 2021; 12:5277. [PMID: 34489474 PMCID: PMC8421416 DOI: 10.1038/s41467-021-25570-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
The pyruvate dehydrogenase complex (PDHc) links glycolysis to the citric acid cycle by converting pyruvate into acetyl-coenzyme A. PDHc encompasses three enzymatically active subunits, namely pyruvate dehydrogenase, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase. Dihydrolipoyl transacetylase is a multidomain protein comprising a varying number of lipoyl domains, a peripheral subunit-binding domain, and a catalytic domain. It forms the structural core of the complex, provides binding sites for the other enzymes, and shuffles reaction intermediates between the active sites through covalently bound lipoyl domains. The molecular mechanism by which this shuttling occurs has remained elusive. Here, we report a cryo-EM reconstruction of the native E. coli dihydrolipoyl transacetylase core in a resting state. This structure provides molecular details of the assembly of the core and reveals how the lipoyl domains interact with the core at the active site.
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Affiliation(s)
- Jana Škerlová
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Berndtsson
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Hendrik Nolte
- grid.419502.b0000 0004 0373 6590Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Martin Ott
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.8761.80000 0000 9919 9582Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Pål Stenmark
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden ,grid.4514.40000 0001 0930 2361Department of Experimental Medical Science, Lund University, Lund, Sweden
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4
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Moxley WC, Eiteman MA. Pyruvate Production by Escherichia coli by Use of Pyruvate Dehydrogenase Variants. Appl Environ Microbiol 2021; 87:e0048721. [PMID: 33863707 PMCID: PMC8315933 DOI: 10.1128/aem.00487-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/10/2021] [Indexed: 11/20/2022] Open
Abstract
Altering metabolic flux at a key branch point in metabolism has commonly been accomplished through gene knockouts or by modulating gene expression. An alternative approach to direct metabolic flux preferentially toward a product is decreasing the activity of a key enzyme through protein engineering. In Escherichia coli, pyruvate can accumulate from glucose when carbon flux through the pyruvate dehydrogenase complex is suppressed. Based on this principle, 16 chromosomally expressed AceE variants were constructed in E. coli C and compared for growth rate and pyruvate accumulation using glucose as the sole carbon source. To prevent conversion of pyruvate to other products, the strains also contained deletions in two nonessential pathways: lactate dehydrogenase (ldhA) and pyruvate oxidase (poxB). The effect of deleting phosphoenolpyruvate synthase (ppsA) on pyruvate assimilation was also examined. The best pyruvate-accumulating strains were examined in controlled batch and continuous processes. In a nitrogen-limited chemostat process at steady-state growth rates of 0.15 to 0.28 h-1, an engineered strain expressing the AceE[H106V] variant accumulated pyruvate at a yield of 0.59 to 0.66 g pyruvate/g glucose with a specific productivity of 0.78 to 0.92 g pyruvate/g cells·h. These results provide proof of concept that pyruvate dehydrogenase complex variants can effectively shift carbon flux away from central carbon metabolism to allow pyruvate accumulation. This approach can potentially be applied to other key enzymes in metabolism to direct carbon toward a biochemical product. IMPORTANCE Microbial production of biochemicals from renewable resources has become an efficient and cost-effective alternative to traditional chemical synthesis methods. Metabolic engineering tools are important for optimizing a process to perform at an economically feasible level. This study describes an additional tool to modify central metabolism and direct metabolic flux to a product. We have shown that variants of the pyruvate dehydrogenase complex can direct metabolic flux away from cell growth to increase pyruvate production in Escherichia coli. This approach could be paired with existing strategies to optimize metabolism and create industrially relevant and economically feasible processes.
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Affiliation(s)
- W. Chris Moxley
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Mark A. Eiteman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, Georgia, USA
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5
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Horvath N, Vilkhovoy M, Wayman JA, Calhoun K, Swartz J, Varner JD. Toward a genome scale sequence specific dynamic model of cell-free protein synthesis in Escherichia coli. Metab Eng Commun 2019; 10:e00113. [PMID: 32280586 PMCID: PMC7136494 DOI: 10.1016/j.mec.2019.e00113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 11/09/2022] Open
Abstract
In this study, we developed a dynamic mathematical model of E. coli cell-free protein synthesis (CFPS). Model parameters were estimated from a dataset consisting of glucose, organic acids, energy species, amino acids, and protein product, chloramphenicol acetyltransferase (CAT) measurements. The model was successfully trained to simulate these measurements, especially those of the central carbon metabolism. We then used the trained model to evaluate the performance, e.g., the yield and rates of protein production. CAT was produced with an energy efficiency of 12%, suggesting that the process could be further optimized. Reaction group knockouts showed that protein productivity was most sensitive to the oxidative phosphorylation and glycolysis/gluconeogenesis pathways. Amino acid biosynthesis was also important for productivity, while overflow metabolism and TCA cycle affected the overall system state. In addition, translation was more important to productivity than transcription. Finally, CAT production was robust to allosteric control, as were most of the predicted metabolite concentrations; the exceptions to this were the concentrations of succinate and malate, and to a lesser extent pyruvate and acetate, which varied from the measured values when allosteric control was removed. This study is the first to use kinetic modeling to predict dynamic protein production in a cell-free E. coli system, and could provide a foundation for genome scale, dynamic modeling of cell-free E. coli protein synthesis. Protein production is biphasic, powered initially by glucose and later by pyruvate. Protein is produced with an energy efficiency of only 12%. Protein productivity is most sensitive to oxidative phosphorylation and glycolysis. Protein production is robust to allosteric control.
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Affiliation(s)
- Nicholas Horvath
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Michael Vilkhovoy
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Joseph A Wayman
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, 14853, USA
| | - Kara Calhoun
- School of Chemical Engineering, Stanford University, Stanford, CA, 94395, USA
| | - James Swartz
- School of Chemical Engineering, Stanford University, Stanford, CA, 94395, USA
| | - Jeffrey D Varner
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
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6
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DeColli AA, Zhang X, Heflin KL, Jordan F, Freel Meyers CL. Active Site Histidines Link Conformational Dynamics with Catalysis on Anti-Infective Target 1-Deoxy-d-xylulose 5-Phosphate Synthase. Biochemistry 2019; 58:4970-4982. [PMID: 31724401 DOI: 10.1021/acs.biochem.9b00878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The product of 1-deoxy-d-xyluose 5-phosphate (DXP) synthase, DXP, feeds into the bacterial biosynthesis of isoprenoids, thiamin diphosphate (ThDP), and pyridoxal phosphate. DXP is essential for human pathogens but not utilized by humans; thus, DXP synthase is an attractive anti-infective target. The unique ThDP-dependent mechanism and structure of DXP synthase offer ideal opportunities for selective targeting. Upon reaction with pyruvate, DXP synthase uniquely stabilizes the predecarboxylation intermediate, C2α-lactylThDP (LThDP), in a closed conformation. Subsequent binding of d-glyceraldehyde 3-phosphate induces an open conformation that is proposed to destabilize LThDP, triggering decarboxylation. Evidence for the closed and open conformations has been revealed by hydrogen-deuterium exchange mass spectrometry and X-ray crystallography, which indicate that H49 and H299 are involved in conformational dynamics and movement of the fork and spoon motifs away from the active site is important for the closed-to-open transition. Interestingly, H49 and H299 are critical for DXP formation and interact with the predecarboxylation intermediate in the closed conformation. H299 is removed from the active site in the open conformation of the postdecarboxylation state. In this study, we show that substitution at H49 and H299 negatively impacts LThDP formation by shifting the conformational equilibrium of DXP synthase toward an open conformation. We also present a method for monitoring the dynamics of the spoon motif that uncovered a previously undetected role for H49 in coordinating the closed conformation. Overall, our results suggest that H49 and H299 are critical for the closed, predecarboxylation state providing the first direct link between catalysis and conformational dynamics.
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Affiliation(s)
- Alicia A DeColli
- Department of Pharmacology and Molecular Sciences , The Johns Hopkins University School of Medicine , Baltimore , Maryland 21205 , United States
| | - Xu Zhang
- Department of Chemistry , Rutgers University , Newark , New Jersey 07102 , United States
| | - Kathryn L Heflin
- Department of Pharmacology and Molecular Sciences , The Johns Hopkins University School of Medicine , Baltimore , Maryland 21205 , United States
| | - Frank Jordan
- Department of Chemistry , Rutgers University , Newark , New Jersey 07102 , United States
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences , The Johns Hopkins University School of Medicine , Baltimore , Maryland 21205 , United States
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7
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Wagner T, Boyko A, Alzari PM, Bunik VI, Bellinzoni M. Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts. J Struct Biol 2019; 208:182-190. [PMID: 31476368 DOI: 10.1016/j.jsb.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/22/2019] [Accepted: 08/29/2019] [Indexed: 11/17/2022]
Abstract
Mycobacterial KGD, the thiamine diphosphate (ThDP)-dependent E1o component of the 2-oxoglutarate dehydrogenase complex (OGDHC), is known to undergo significant conformational changes during catalysis with two distinct conformational states, previously named as the early and late state. In this work, we employ two phosphonate analogues of 2-oxoglutarate (OG), i.e. succinyl phosphonate (SP) and phosphono ethyl succinyl phosphonate (PESP), as tools to isolate the first catalytic steps and understand the significance of conformational transitions for the enzyme regulation. The kinetics showed a more efficient inhibition of mycobacterial E1o by SP (Ki 0.043 ± 0.013 mM) than PESP (Ki 0.88 ± 0.28 mM), consistent with the different circular dichroism spectra of the corresponding complexes. PESP allowed us to get crystallographic snapshots of the Michaelis-like complex, the first one for 2-oxo acid dehydrogenases, followed by the covalent adduction of the inhibitor to ThDP, mimicking the pre-decarboxylation complex. In addition, covalent ThDP-phosphonate complexes obtained with both compounds by co-crystallization were in the late conformational state, probably corresponding to slowly dissociating enzyme-inhibitor complexes. We discuss the relevance of these findings in terms of regulatory features of the mycobacterial E1o enzymes, and in the perspective of developing tools for species-specific metabolic regulation.
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Affiliation(s)
- Tristan Wagner
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France
| | - Alexandra Boyko
- A.N. Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France
| | - Victoria I Bunik
- A.N. Belozersky Institute of Physicochemical Biology and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75724 Paris, France.
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8
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Chen PYT, DeColli AA, Freel Meyers CL, Drennan CL. X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate. J Biol Chem 2019; 294:12405-12414. [PMID: 31239351 PMCID: PMC6699841 DOI: 10.1074/jbc.ra119.009321] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/16/2019] [Indexed: 01/07/2023] Open
Abstract
1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) uses thiamine diphosphate (ThDP) to convert pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) into 1-deoxy-d-xylulose 5-phosphate (DXP), an essential bacterial metabolite. DXP is not utilized by humans; hence, DXPS has been an attractive antibacterial target. Here, we investigate DXPS from Deinococcus radiodurans (DrDXPS), showing that it has similar kinetic parameters Kmd-GAP and Kmpyruvate (54 ± 3 and 11 ± 1 μm, respectively) and comparable catalytic activity (kcat = 45 ± 2 min-1) with previously studied bacterial DXPS enzymes and employing it to obtain missing structural data on this enzyme family. In particular, we have determined crystallographic snapshots of DrDXPS in two states along the reaction coordinate: a structure of DrDXPS bound to C2α-phosphonolactylThDP (PLThDP), mimicking the native pre-decarboxylation intermediate C2α-lactylThDP (LThDP), and a native post-decarboxylation state with a bound enamine intermediate. The 1.94-Å-resolution structure of PLThDP-bound DrDXPS delineates how two active-site histidine residues stabilize the LThDP intermediate. Meanwhile, the 2.40-Å-resolution structure of an enamine intermediate-bound DrDXPS reveals how a previously unknown 17-Å conformational change removes one of the two histidine residues from the active site, likely triggering LThDP decarboxylation to form the enamine intermediate. These results provide insight into how the bi-substrate enzyme DXPS limits side reactions by arresting the reaction on the less reactive LThDP intermediate when its cosubstrate is absent. They also offer a molecular basis for previous low-resolution experimental observations that correlate decarboxylation of LThDP with protein conformational changes.
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Affiliation(s)
- Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Alicia A. DeColli
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, To whom correspondence may be addressed:
Dept. of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205. Tel.:
410-502-4807; Fax:
410-955-3023; E-mail:
| | - Catherine L. Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, A Howard Hughes Medical Institute investigator and a senior fellow of the Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR). To whom correspondence may be addressed:
Depts. of Biology and Chemistry, Massachusetts Institute of Technology, 31 Ames St., Bldg. 68-680, Cambridge, MA 02139. Tel.:
617-253-5622; Fax:
617-258-7847; E-mail:
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9
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Identification of functional interactome of a key cell division regulatory protein CedA of E.coli. Int J Biol Macromol 2017; 106:763-767. [PMID: 28818726 DOI: 10.1016/j.ijbiomac.2017.08.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/23/2022]
Abstract
Cell division is compromised in DnaAcos mutant Escherichia coli cells that results in filamentous cell morphology. This is countered by over-expression of CedA protein that induces cytokinesis and thus, regular cell morphology is regained; however via an unknown mechanism. To understand the process systematically, exact role of CedA should be deciphered. Protein interactions are crucial for functional organization of a cell and their identification helps in revealing exact function(s) of a protein and its binding partners. Thus, this study was intended to identify CedA binding proteins (CBPs) to gain more clues of CedA function. We isolated CBPs by pull down assay using purified recombinant CedA and identified nine CBPs by mass spectrometric analysis (MALDI-TOF MS and LC-MS/MS), viz. PDHA1, RL2, DNAK, LPP, RPOB, G6PD, GLMS, RL3 and YBCJ. Based on CBPs identified, we hypothesize that CedA plays a crucial and multifaceted role in cell cycle regulation and specific pathways in which CedA participates may include transcription and energy metabolism. However, further validation through in-vitro and in-vivo experiments is necessary. In conclusion, identification of CBPs may help us in deciphering mechanism of CedA mediated cell division during chromosomal DNA over-replication.
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10
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Mechanistic and Structural Insight to an Evolved Benzoylformate Decarboxylase with Enhanced Pyruvate Decarboxylase Activity. Catalysts 2016. [DOI: 10.3390/catal6120190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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11
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Scott RA, Lindow SE. Transcriptional control of quorum sensing and associated metabolic interactions inPseudomonas syringaestrain B728a. Mol Microbiol 2016; 99:1080-98. [DOI: 10.1111/mmi.13289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/02/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Russell A. Scott
- Department of Plant and Microbial Biology; University of California; 111 Koshland Hall Berkeley CA 94720-3102 USA
| | - Steven E. Lindow
- Department of Plant and Microbial Biology; University of California; 111 Koshland Hall Berkeley CA 94720-3102 USA
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12
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Willrodt C, Hoschek A, Bühler B, Schmid A, Julsing MK. Decoupling production from growth by magnesium sulfate limitation boosts de novo limonene production. Biotechnol Bioeng 2015; 113:1305-14. [PMID: 26574166 DOI: 10.1002/bit.25883] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/08/2015] [Indexed: 01/23/2023]
Abstract
The microbial production of isoprenoids has recently developed into a prime example for successful bottom-up synthetic biology or top-down systems biology strategies. Respective fermentation processes typically rely on growing recombinant microorganisms. However, the fermentative production of isoprenoids has to compete with cellular maintenance and growth for carbon and energy. Non-growing but metabolically active E. coli cells were evaluated in this study as alternative biocatalyst configurations to reduce energy and carbon loss towards biomass formation. The use of non-growing cells in an optimized fermentation medium resulted in more than fivefold increased specific limonene yields on cell dry weight and glucose, as compared to the traditional growing-cell-approach. Initially, the stability of the resting-cell activity was limited. This instability was overcome via the optimization of the minimal fermentation medium enabling high and stable limonene production rates for up to 8 h and a high specific yield of ≥50 mg limonene per gram cell dry weight. Omitting MgSO4 from the fermentation medium was very promising to prohibit growth and allow high productivities. Applying a MgSO4 -limitation also improved limonene formation by growing cells during non-exponential growth involving a reduced biomass yield on glucose and a fourfold increase in specific limonene yields on biomass as compared to non-limited cultures. The control of microbial growth via the medium composition was identified as a key but yet underrated strategy for efficient isoprenoid production. Biotechnol. Bioeng. 2016;113: 1305-1314. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Christian Willrodt
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.,Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Anna Hoschek
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Bruno Bühler
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Andreas Schmid
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.
| | - Mattijs K Julsing
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
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13
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Arjunan P, Wang J, Nemeria NS, Reynolds S, Brown I, Chandrasekhar K, Calero G, Jordan F, Furey W. Novel binding motif and new flexibility revealed by structural analyses of a pyruvate dehydrogenase-dihydrolipoyl acetyltransferase subcomplex from the Escherichia coli pyruvate dehydrogenase multienzyme complex. J Biol Chem 2014; 289:30161-76. [PMID: 25210042 DOI: 10.1074/jbc.m114.592915] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli pyruvate dehydrogenase multienzyme complex contains multiple copies of three enzymatic components, E1p, E2p, and E3, that sequentially carry out distinct steps in the overall reaction converting pyruvate to acetyl-CoA. Efficient functioning requires the enzymatic components to assemble into a large complex, the integrity of which is maintained by tethering of the displaced, peripheral E1p and E3 components to the E2p core through non-covalent binding. We here report the crystal structure of a subcomplex between E1p and an E2p didomain containing a hybrid lipoyl domain along with the peripheral subunit-binding domain responsible for tethering to the core. In the structure, a region at the N terminus of each subunit in the E1p homodimer previously unseen due to crystallographic disorder was observed, revealing a new folding motif involved in E1p-E2p didomain interactions, and an additional, unexpected, flexibility was discovered in the E1p-E2p didomain subcomplex, both of which probably have consequences in the overall multienzyme complex assembly. This represents the first structure of an E1p-E2p didomain subcomplex involving a homodimeric E1p, and the results may be applicable to a large range of complexes with homodimeric E1 components. Results of HD exchange mass spectrometric experiments using the intact, wild type 3-lipoyl E2p and E1p are consistent with the crystallographic data obtained from the E1p-E2p didomain subcomplex as well as with other biochemical and NMR data reported from our groups, confirming that our findings are applicable to the entire E1p-E2p assembly.
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Affiliation(s)
| | - Junjie Wang
- the Department of Chemistry, Rutgers University, Newark, New Jersey 07102, and
| | - Natalia S Nemeria
- the Department of Chemistry, Rutgers University, Newark, New Jersey 07102, and
| | - Shelley Reynolds
- Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Ian Brown
- Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | | | - Guillermo Calero
- Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Frank Jordan
- the Department of Chemistry, Rutgers University, Newark, New Jersey 07102, and
| | - William Furey
- From the Departments of Pharmacology and Chemical Biology and the Veterans Affairs Medical Center, Pittsburgh, Pennsylvania 15240
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14
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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: 18] [Impact Index Per Article: 1.8] [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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15
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Basta LAB, Patel H, Kakalis L, Jordan F, Meyers CLF. Defining critical residues for substrate binding to 1-deoxy-D-xylulose 5-phosphate synthase--active site substitutions stabilize the predecarboxylation intermediate C2α-lactylthiamin diphosphate. FEBS J 2014; 281:2820-2837. [PMID: 24767541 PMCID: PMC4065394 DOI: 10.1111/febs.12823] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 04/06/2014] [Accepted: 04/18/2014] [Indexed: 10/25/2022]
Abstract
1-Deoxy-D-xylulose 5-phosphate (DXP) synthase catalyzes the formation of DXP from pyruvate and D-glyceraldehyde 3-phosphate (GraP) in a thiamin diphosphate-dependent manner, and is the first step in the essential pathway to isoprenoids in human pathogens. Understanding the mechanism of this unique enzyme is critical for developing new anti-infective agents that selectively target isoprenoid biosynthesis. The present study used mutagenesis and a combination of protein fluorescence, CD and kinetics experiments to investigate the roles of Arg420, Arg478 and Tyr392 in substrate binding and catalysis. The results support a random sequential, preferred order mechanism, and predict that Arg420 and Arg478 are involved in binding of the acceptor substrate, GraP. D-Glyceraldehyde, an alternative acceptor substrate lacking the phosphoryl group predicted to interact with Arg420 and Arg478, also accelerates decarboxylation of the predecarboxylation intermediate C2α-lactylthiamin diphosphate (LThDP) on DXP synthase, indicating that this binding interaction is not absolutely required, and that the hydroxyaldehyde sufficiently triggers decarboxylation. Unexpectedly, Tyr392 contributes to GraP affinity, and is not required for LThDP formation or its GraP-promoted decarboxylation. Time-resolved CD spectroscopy and NMR experiments indicate that LThDP is significantly stabilized on R420A and Y392F variants as compared with wild-type DXP synthase in the absence of acceptor substrate, but these substitutions do not appear to affect the rate of GraP-promoted LThDP decarboxylation in the presence of high levels of GraP, and LThDP formation remains the rate-limiting step. These results suggest a role of these residues in promoting GraP binding, which in turn facilitates decarboxylation, and also highlight interesting differences between DXP synthase and other thiamin diphosphate-dependent enzymes.
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Affiliation(s)
- Leighanne A. Brammer Basta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hetalben Patel
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Lazaros Kakalis
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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16
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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: 379] [Impact Index Per Article: 37.9] [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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17
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A dual conformation of the post-decarboxylation intermediate is associated with distinct enzyme states in mycobacterial KGD (α-ketoglutarate decarboxylase). Biochem J 2014; 457:425-34. [PMID: 24171907 DOI: 10.1042/bj20131142] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
α-Ketoacid dehydrogenases are large multi-enzyme machineries that orchestrate the oxidative decarboxylation of α-ketoacids with the concomitant production of acyl-CoA and NADH. The first reaction, catalysed by α-ketoacid decarboxylases (E1 enzymes), needs a thiamine diphosphate cofactor and represents the overall rate-limiting step. Although the catalytic cycles of E1 from the pyruvate dehydrogenase (E1p) and branched-chain α-ketoacid dehydrogenase (E1b) complexes have been elucidated, little structural information is available on E1o, the first component of the α-ketoglutarate dehydrogenase complex, despite the central role of this complex at the branching point between the TCA (tricarboxylic acid) cycle and glutamate metabolism. In the present study, we provide structural evidence that MsKGD, the E1o (α-ketoglutarate decarboxylase) from Mycobacterium smegmatis, shows two conformations of the post-decarboxylation intermediate, each one associated with a distinct enzyme state. We also provide an overall picture of the catalytic cycle, reconstructed by either crystallographic snapshots or modelling. The results of the present study show that the conformational change leading the enzyme from the initial (early) to the late state, although not required for decarboxylation, plays an essential role in catalysis and possibly in the regulation of mycobacterial E1o.
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18
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Environmental dependence of stationary-phase metabolism in Bacillus subtilis and Escherichia coli. Appl Environ Microbiol 2014; 80:2901-9. [PMID: 24584250 DOI: 10.1128/aem.00061-14] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
When microbes lack the nutrients necessary for growth, they enter stationary phase. In cases when energy sources are still present in the environment, they must decide whether to continue to use their metabolic program to harvest the available energy. Here we characterized the metabolic response to a variety of types of nutrient starvation in Escherichia coli and Bacillus subtilis. We found that E. coli exhibits a range of phenotypes, with the lowest metabolic rates under nitrogen starvation and highest rates under magnesium starvation. In contrast, the phenotype of B. subtilis was dominated by its decision to form metabolically inactive endospores. While its metabolic rates under most conditions were thus lower than those of E. coli, when sporulation was suppressed by a genetic perturbation or an unnatural starvation condition, the situation was reversed. To further probe stationary-phase metabolism, we used quantitative metabolomics to investigate possible small-molecule signals that may regulate the metabolic rate of E. coli and initiate sporulation in B. subtilis. We hypothesize a role for phosphoenolpyruvate (PEP) in regulating E. coli glucose uptake and for the redox cofactors NAD(H) and NADP(H) in initiation of sporulation. Our work is directly relevant to synthetic biology and metabolic engineering, where active metabolism during stationary phase, which uncouples production from growth, remains an elusive goal.
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19
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Smith JM, Warrington NV, Vierling RJ, Kuhn ML, Anderson WF, Koppisch AT, Freel Meyers CL. Targeting DXP synthase in human pathogens: enzyme inhibition and antimicrobial activity of butylacetylphosphonate. J Antibiot (Tokyo) 2014; 67:77-83. [PMID: 24169798 PMCID: PMC3946878 DOI: 10.1038/ja.2013.105] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 09/20/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022]
Abstract
The unique methylerythritol phosphate pathway for isoprenoid biosynthesis is essential in most bacterial pathogens. The first enzyme in this pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes a distinct thiamin diphosphate (ThDP)-dependent reaction to form DXP from D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate and represents a potential anti-infective drug target. We have previously demonstrated that the unnatural bisubstrate analog, butylacetylphosphonate (BAP), exhibits selective inhibition of Escherichia coli DXP synthase over mammalian ThDP-dependent enzymes. Here, we report the selective inhibition by BAP against recombinant DXP synthase homologs from Mycobacterium tuberculosis, Yersinia pestis and Salmonella enterica. We also demonstrate antimicrobial activity of BAP against both Gram-negative and Gram-positive strains (including E. coli, S. enterica and Bacillus anthracis), and several clinically isolated pathogens. Our results suggest a mechanism of action involving inhibition of DXP synthase and show that BAP acts synergistically with established antimicrobial agents, highlighting a potential strategy to combat emerging resistance in bacterial pathogens.
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Affiliation(s)
- Jessica M Smith
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nicole V Warrington
- Deptartment of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Ryan J Vierling
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Misty L Kuhn
- Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL, USA
| | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases, Northwestern Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Chicago, IL, USA
| | - Andrew T Koppisch
- Deptartment of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Caren L Freel Meyers
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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20
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Nuclear magnetic resonance approaches in the study of 2-oxo acid dehydrogenase multienzyme complexes--a literature review. Molecules 2013; 18:11873-903. [PMID: 24077172 PMCID: PMC6270654 DOI: 10.3390/molecules181011873] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/14/2013] [Accepted: 09/16/2013] [Indexed: 11/17/2022] Open
Abstract
The 2-oxoacid dehydrogenase complexes (ODHc) consist of multiple copies of three enzyme components: E1, a 2-oxoacid decarboxylase; E2, dihydrolipoyl acyl-transferase; and E3, dihydrolipoyl dehydrogenase, that together catalyze the oxidative decarboxylation of 2-oxoacids, in the presence of thiamin diphosphate (ThDP), coenzyme A (CoA), Mg²⁺ and NAD⁺, to generate CO₂, NADH and the corresponding acyl-CoA. The structural scaffold of the complex is provided by E2, with E1 and E3 bound around the periphery. The three principal members of the family are pyruvate dehydrogenase (PDHc), 2-oxoglutarate dehydrogenase (OGDHc) and branched-chain 2-oxo acid dehydrogenase (BCKDHc). In this review, we report application of NMR-based approaches to both mechanistic and structural issues concerning these complexes. These studies revealed the nature and reactivity of transient intermediates on the enzymatic pathway and provided site-specific information on the architecture and binding specificity of the domain interfaces using solubilized truncated domain constructs of the multi-domain E2 component in its interactions with the E1 and E3 components. Where studied, NMR has also provided information about mobile loops and the possible relationship of mobility and catalysis.
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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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Chandrasekhar K, Wang J, Arjunan P, Sax M, Park YH, Nemeria NS, Kumaran S, Song J, Jordan F, Furey W. Insight to the interaction of the dihydrolipoamide acetyltransferase (E2) core with the peripheral components in the Escherichia coli pyruvate dehydrogenase complex via multifaceted structural approaches. J Biol Chem 2013; 288:15402-17. [PMID: 23580650 DOI: 10.1074/jbc.m113.466789] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Multifaceted structural approaches were undertaken to investigate interaction of the E2 component with E3 and E1 components from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), as a representative of the PDHc from Gram-negative bacteria. The crystal structure of E3 at 2.5 Å resolution reveals similarity to other E3 structures and was an important starting point for understanding interaction surfaces between E3 and E2. Biochemical studies revealed that R129E-E2 and R150E-E2 substitutions in the peripheral subunit-binding domain (PSBD) of E2 greatly diminished PDHc activity, affected interactions with E3 and E1 components, and affected reductive acetylation of E2. Because crystal structures are unavailable for any complete E2-containing complexes, peptide-specific hydrogen/deuterium exchange mass spectrometry was used to identify loci of interactions between 3-lipoyl E2 and E3. Two peptides from the PSBD, including Arg-129, and three peptides from E3 displayed statistically significant reductions in deuterium uptake resulting from interaction between E3 and E2. Of the peptides identified on E3, two were from the catalytic site, and the third was from the interface domain, which for all known E3 structures is believed to interact with the PSBD. NMR clearly demonstrates that there is no change in the lipoyl domain structure on complexation with E3. This is the first instance where the entire wild-type E2 component was employed to understand interactions with E3. A model for PSBD-E3 binding was independently constructed and found to be consistent with the importance of Arg-129, as well as revealing other electrostatic interactions likely stabilizing this complex.
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Affiliation(s)
- Krishnamoorthy Chandrasekhar
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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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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Balakrishnan A, Gao Y, Moorjani P, Nemeria NS, Tittmann K, Jordan F. Bifunctionality of the thiamin diphosphate cofactor: assignment of tautomeric/ionization states of the 4'-aminopyrimidine ring when various intermediates occupy the active sites during the catalysis of yeast pyruvate decarboxylase. J Am Chem Soc 2012; 134:3873-85. [PMID: 22300533 PMCID: PMC3295232 DOI: 10.1021/ja211139c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiamin diphosphate (ThDP) dependent enzymes perform crucial C-C bond forming and breaking reactions in sugar and amino acid metabolism and in biosynthetic pathways via a sequence of ThDP-bound covalent intermediates. A member of this superfamily, yeast pyruvate decarboxylase (YPDC) carries out the nonoxidative decarboxylation of pyruvate and is mechanistically a simpler ThDP enzyme. YPDC variants created by substitution at the active center (D28A, E51X, and E477Q) and on the substrate activation pathway (E91D and C221E) display varying activity, suggesting that they stabilize different covalent intermediates. To test the role of both rings of ThDP in YPDC catalysis (the 4'-aminopyrimidine as acid-base, and thiazolium as electrophilic covalent catalyst), we applied a combination of steady state and time-resolved circular dichroism experiments (assessing the state of ionization and tautomerization of enzyme-bound ThDP-related intermediates), and chemical quench of enzymatic reaction mixtures followed by NMR characterization of the ThDP-bound intermediates released from YPDC (assessing occupancy of active centers by these intermediates and rate-limiting steps). Results suggest the following: (1) Pyruvate and analogs induce active site asymmetry in YPDC and variants. (2) The rare 1',4'-iminopyrimidine ThDP tautomer participates in formation of ThDP-bound intermediates. (3) Propionylphosphinate also binds at the regulatory site and its binding is reflected by catalytic events at the active site 20 Å away. (4) YPDC stabilizes an electrostatic model for the 4'-aminopyrimidinium ionization state, an important contribution of the protein to catalysis. The combination of tools used provides time-resolved details about individual events during ThDP catalysis; the methods are transferable to other ThDP superfamily members.
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Affiliation(s)
| | - Yuhong Gao
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Prerna Moorjani
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | | | - Kai Tittmann
- Albrecht-von-Haller Institute & Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, D-37077 Göttingen, Germany
| | - Frank Jordan
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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25
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Brammer LA, Smith JM, Wade H, Meyers CF. 1-Deoxy-D-xylulose 5-phosphate synthase catalyzes a novel random sequential mechanism. J Biol Chem 2011; 286:36522-31. [PMID: 21878632 DOI: 10.1074/jbc.m111.259747] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Emerging resistance of human pathogens to anti-infective agents make it necessary to develop new agents to treat infection. The methylerythritol phosphate pathway has been identified as an anti-infective target, as this essential isoprenoid biosynthetic pathway is widespread in human pathogens but absent in humans. The first enzyme of the pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes the formation of DXP via condensation of D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate in a thiamine diphosphate-dependent manner. Structural analysis has revealed a unique domain arrangement suggesting opportunities for the selective targeting of DXP synthase; however, reports on the kinetic mechanism are conflicting. Here, we present the results of tryptophan fluorescence binding and kinetic analyses of DXP synthase and propose a new model for substrate binding and mechanism. Our results are consistent with a random sequential kinetic mechanism, which is unprecedented in this enzyme class.
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Affiliation(s)
- Leighanne A Brammer
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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26
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Song J, Park YH, Nemeria NS, Kale S, Kakalis L, Jordan F. Nuclear magnetic resonance evidence for the role of the flexible regions of the E1 component of the pyruvate dehydrogenase complex from gram-negative bacteria. J Biol Chem 2009; 285:4680-94. [PMID: 19996100 DOI: 10.1074/jbc.m109.082842] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most bacterial pyruvate dehydrogenase complexes from either gram-positive or gram-negative bacteria have E1 components with an alpha(2) homodimeric quaternary structure. In a sequel to our previous publications, we present the first NMR study on the flexible regions of the E1 component from Escherichia coli and its biological relevance. We report sequence-specific NMR assignments for 6 residues in the N-terminal 1-55 region and for a glycine in each of the two mobile active center loops of the E1 component, a 200-kDa homodimer. This was accomplished by using site-specific substitutions and appropriate labeling patterns along with a peptide with the sequence corresponding to the N-terminal 1-35 amino acids of the E1 component. To study the functions of these mobile regions, we also examined the spectra in the presence of (a) a reaction intermediate analog known to affect the mobility of the active center loops, (b) an E2 component construct consisting of a lipoyl domain and peripheral subunit binding domain, and (c) a peptide corresponding to the amino acid sequence of the E2 peripheral subunit binding domain. Deductions from the NMR studies are in excellent agreement with our functional finding, providing a clear indication that the N-terminal region of the E1 interacts with the E2 peripheral subunit binding domain and that this interaction precedes reductive acetylation. The results provide the first structural support to the notion that the N-terminal region of the E1 component of this entire class of bacterial pyruvate dehydrogenase complexes is responsible for binding the E2 component.
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Affiliation(s)
- Jaeyoung Song
- Department of Chemistry, Rutgers, the State University of New Jersey, Newark, New Jersey 07102, USA
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27
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Jordan F, Arjunan P, Kale S, Nemeria NS, Furey W. Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis. JOURNAL OF MOLECULAR CATALYSIS. B, ENZYMATIC 2009; 61:14-22. [PMID: 20160956 PMCID: PMC2759092 DOI: 10.1016/j.molcatb.2009.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The region encompassing residues 401-413 on the E1 component of the pyruvate dehydrogenase multienzyme complex from Escherichia coli comprises a loop (the inner loop) which was not seen in the X-ray structure in the presence of thiamin diphosphate, the required cofactor for the enzyme. This loop is seen in the presence of a stable analogue of the pre-decarboxylation intermediate, the covalent adduct between the substrate analogue methyl acetylphosphonate and thiamin diphosphate, C2α-phosphonolactylthiamin diphosphate. It has been shown that the residue H407 and several other residues on this loop are required to reduce the mobility of the loop so electron density corresponding to it can be seen once the pre-decarboxylation intermediate is formed. Concomitantly, the loop encompassing residues 541-557 (the outer loop) appears to work in tandem with the inner loop and there is a hydrogen bond between the two loops ensuring their correlated motion. The inner loop was shown to: a) sequester the active center from carboligase side reactions; b) assist the interaction between the E1 and the E2 components, thereby affecting the overall reaction rate of the entire multienzyme complex; c) control substrate access to the active center. Using viscosity effects on kinetics it was shown that formation of the pre-decarboxylation intermediate is specifically affected by loop movement. A cysteine-less variant was created for the E1 component, onto which cysteines were substituted at selected loop positions. Introducing an electron spin resonance spin label and an (19)F NMR label onto these engineered cysteines, the loop mobility was examined: a) both methods suggested that in the absence of ligand, the loop exists in two conformations; b) line-shape analysis of the NMR signal at different temperatures, enabled estimation of the rate constant for loop movement, and this rate constant was found to be of the same order of magnitude as the turnover number for the enzyme under the same conditions. Furthermore, this analysis gave important insights into rate-limiting thermal loop dynamics. Overall, the results suggest that the dynamic properties correlate with catalytic events on the E1 component of the pyruvate dehydrogenase complex.
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Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | - Palaniappa Arjunan
- Biocrystallography Laboratory, Veterans Affairs Medical Center, Pittsburgh, Pennsylvania 15240
| | - Sachin Kale
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102
| | | | - William Furey
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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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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29
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Agyei-Owusu K, Leeper FJ. Thiamin diphosphate in biological chemistry: analogues of thiamin diphosphate in studies of enzymes and riboswitches. FEBS J 2009; 276:2905-16. [PMID: 19490097 DOI: 10.1111/j.1742-4658.2009.07018.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The role of thiamin diphosphate (ThDP) as a cofactor for enzymes has been known for many decades. This minireview covers the progress made in understanding the catalytic mechanism of ThDP-dependent enzymes through the use of ThDP analogues. Many such analogues have been synthesized and have provided information on the functional groups necessary for the binding and catalytic activity of the cofactor. Through these studies, the important role of hydrophobic interactions in stabilizing reaction intermediates in the catalytic cycle has been recognized. Stable analogues of intermediates in the ThDP-catalysed reaction mechanism have also been synthesized and crystallographic studies using these analogues have allowed enzyme structures to be solved that represent snapshots of the reaction in progress. As well as providing mechanistic information about ThDP-dependent enzymes, many analogues are potent inhibitors of these enzymes. The potential of these compounds as therapeutic targets and as important herbicidal agents is discussed. More recently, the way that ThDP regulates the genes for its own biosynthesis through the action of riboswitches has been discovered. This opens a new branch of thiamin research with the potential to provide new therapeutic targets in the fight against infection.
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30
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Chakraborty S, Nemeria NS, Balakrishnan A, Brandt GS, Kneen MM, Yep A, McLeish MJ, Kenyon GL, Petsko GA, Ringe D, Jordan F. Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase. Biochemistry 2009; 48:981-94. [PMID: 19140682 DOI: 10.1021/bi801810h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the enzyme benzoylformate decarboxylase (BFDC), which carries out a typical thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, was studied with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). Addition of 3-PKB resulted in the appearance of two transient intermediates formed consecutively, the first one to be formed a predecarboxylation ThDP-bound intermediate with lambda(max) at 477 nm, and the second one corresponding to the first postdecarboxylation intermediate the enamine with lambda(max) at 437 nm. The time course of formation/depletion of the PKB-ThDP covalent complex and of the enamine showed that decarboxylation was slower than formation of the PKB-ThDP covalent adduct. When the product of decarboxylation 3-(pyridin-3-yl)acrylaldehyde (PAA) was added to BFDC, again an absorbance with lambda(max) at 473 nm was formed, corresponding to the tetrahedral adduct of PAA with ThDP. Addition of well-formed crystals of BFDC to a solution of PAA resulted in a high resolution (1.34 A) structure of the BFDC-bound adduct of ThDP with PAA confirming the tetrahedral nature at the C2alpha atom, rather than of the enamine, and supporting the assignment of the lambda(max) at 473 nm to the PAA-ThDP adduct. The structure of the PAA-ThDP covalent complex is the first example of a product-ThDP adduct on BFDC. Similar studies with 3-PKB indicated that decarboxylation had taken place. Evidence was also obtained for the slow formation of the enamine intermediate when BFDC was incubated with benzaldehyde, the product of the decarboxylation reaction thus confirming its presence on the reaction pathway.
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Affiliation(s)
- Sumit Chakraborty
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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31
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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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32
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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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33
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Chakraborty S, Nemeria N, Yep A, McLeish MJ, Kenyon GL, Jordan F. Mechanism of benzaldehyde lyase studied via thiamin diphosphate-bound intermediates and kinetic isotope effects. Biochemistry 2008; 47:3800-9. [PMID: 18314961 DOI: 10.1021/bi702302u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Direct spectroscopic observation of thiamin diphosphate-bound intermediates was achieved on the enzyme benzaldehyde lyase, which carries out reversible and highly enantiospecific conversion of ( R)-benzoin to benzaldehyde. The key enamine intermediate could be observed at lambda max 393 nm in the benzoin breakdown direction and in the decarboxylase reaction starting with benzoylformate. With benzaldehyde as substrate, no intermediates could be detected, only formation of benzoin at 314 nm. To probe the rate-limiting step in the direction of ( R)-benzoin synthesis, the (1)H/ (2)H kinetic isotope effect was determined for benzaldehyde labeled at the aldehyde position and found to be small (1.14 +/- 0.03), indicating that ionization of the C2alphaH from C2alpha-hydroxybenzylthiamin diphosphate is not rate limiting. Use of the alternate substrates benzoylformic and phenylpyruvic acids (motivated by the observation that while a carboligase, benzaldehyde lyase could also catalyze the slow decarboxylation of 2-oxo acids) enabled the observation of the substrate-thiamin covalent intermediate via the 1',4'-iminopyrimidine tautomer, characteristic of all intermediates with a tetrahedral C2 substituent on ThDP. The reaction of benzaldehyde lyase with the chromophoric substrate analogue ( E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid and its decarboxylated product ( E)-3-(pyridine-3-yl)acrylaldehyde enabled the detection of covalent adducts with both. Neither adduct underwent further reaction. An important finding of the studies is that all thiamin-related intermediates are in a chiral environment on benzaldehyde lyase as reflected by their circular dichroism signatures.
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Affiliation(s)
- Sumit Chakraborty
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
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34
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Efficient coupling of catalysis and dynamics in the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex. Proc Natl Acad Sci U S A 2008; 105:1158-63. [PMID: 18216265 DOI: 10.1073/pnas.0709328105] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein motions are ubiquitous and are intrinsically coupled to catalysis. Their specific roles, however, remain largely elusive. Dynamic loops at the active center of the E1 component of Escherichia coli pyruvate dehydrogenase multienzyme complex are essential for several catalytic functions starting from a predecarboxylation event and culminating in transfer of the acetyl moiety to the E2 component. Monitoring the kinetics of E1 and its loop variants at various solution viscosities, we show that the rate of a chemical step is modulated by loop dynamics. A cysteine-free E1 construct was site-specifically labeled on the inner loop (residues 401-413), and the EPR nitroxide label revealed ligand-induced conformational dynamics of the loop and a slow "open <--> close" conformational equilibrium in the unliganded state. An (19)F NMR label placed at the same residue revealed motion on the millisecond-second time scale and suggested a quantitative correlation of E1 catalysis and loop dynamics for the 200,000-Da protein. Thermodynamic studies revealed that these motions may promote covalent addition of substrate to the enzyme-bound thiamin diphosphate by reducing the free energy of activation. Furthermore, the global dynamics of E1 presumably regulate and streamline the catalytic steps of the overall complex by inducing an entirely entropic (nonmechanical) negative cooperativity with respect to substrate binding at higher temperatures. Our results are consistent with, and reinforce the hypothesis of, coupling of catalysis and regulation with enzyme dynamics and suggest the mechanism by which it is achieved in a key branchpoint enzyme in sugar metabolism.
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35
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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: 48] [Impact Index Per Article: 2.5] [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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