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Kikuchi A, Nakazato T, Ito K, Nojima Y, Yokoyama T, Iwabuchi K, Bono H, Toyoda A, Fujiyama A, Sato R, Tabunoki H. Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes. BMC Genomics 2017; 18:83. [PMID: 28086791 PMCID: PMC5237310 DOI: 10.1186/s12864-016-3455-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. RESULTS Enolase is an important glycolytic enzyme in all organisms. We used a combination of dry and wet bench processes to identify functional enolases in the silkworm Bombyx mori (BmEno). First, we detected five annotated enolases from public databases using a Hidden Markov Model (HMM) search, and then through cDNA cloning, Northern blotting, and RNA-seq analysis, we revealed three functional enolases in B. mori: BmEno1, BmEno2, and BmEnoC. BmEno1 contained a conserved key amino acid residue for metal binding and substrate binding in other species. However, BmEno2 and BmEnoC showed a change in this key amino acid. Phylogenetic analysis showed that BmEno2 and BmEnoC were distinct from BmEno1 and other enolases, and were distributed only in lepidopteran clusters. BmEno1 was expressed in all of the tissues used in our study. In contrast, BmEno2 was mainly expressed in the testis with some expression in the ovary and suboesophageal ganglion. BmEnoC was weakly expressed in the testis. Quantitative RT-PCR showed that the mRNA expression of BmEno2 and BmEnoC correlated with testis development; thus, BmEno2 and BmEnoC may be related to lepidopteran-specific spermiogenesis. CONCLUSIONS We identified and characterized three functional enolases from public databases with a combination of dry and wet bench processes in the silkworm B. mori. In addition, we determined that BmEno2 and BmEnoC had species-specific functions. Our strategy could be helpful for the detection of minor genes and functional genes in non-model organisms from public databases.
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Affiliation(s)
- Akira Kikuchi
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takeru Nakazato
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Katsuhiko Ito
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Yosui Nojima
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takeshi Yokoyama
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Kikuo Iwabuchi
- Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Hidemasa Bono
- Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Asao Fujiyama
- Center for Information Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Ryoichi Sato
- Graduate School of Bio-Applications and Systems Engineering (BASE), 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Hiroko Tabunoki
- Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
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Williamson T, Adiamah D, Schwartz JM, Stateva L. Exploring the genetic control of glycolytic oscillations in Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2012; 6:108. [PMID: 22920924 PMCID: PMC3497587 DOI: 10.1186/1752-0509-6-108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 07/24/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND A well known example of oscillatory phenomena is the transient oscillations of glycolytic intermediates in Saccharomyces cerevisiae, their regulation being predominantly investigated by mathematical modeling. To our knowledge there has not been a genetic approach to elucidate the regulatory role of the different enzymes of the glycolytic pathway. RESULTS We report that the laboratory strain BY4743 could also be used to investigate this oscillatory phenomenon, which traditionally has been studied using S. cerevisiae X2180. This has enabled us to employ existing isogenic deletion mutants and dissect the roles of isoforms, or subunits of key glycolytic enzymes in glycolytic oscillations. We demonstrate that deletion of TDH3 but not TDH2 and TDH1 (encoding glyceraldehyde-3-phosphate dehydrogenase: GAPDH) abolishes NADH oscillations. While deletion of each of the hexokinase (HK) encoding genes (HXK1 and HXK2) leads to oscillations that are longer lasting with lower amplitude, the effect of HXK2 deletion on the duration of the oscillations is stronger than that of HXK1. Most importantly our results show that the presence of beta (Pfk2) but not that of alpha subunits (Pfk1) of the hetero-octameric enzyme phosphofructokinase (PFK) is necessary to achieve these oscillations. Furthermore, we report that the cAMP-mediated PKA pathway (via some of its components responsible for feedback down-regulation) modulates the activity of glycoytic enzymes thus affecting oscillations. Deletion of both PDE2 (encoding a high affinity cAMP-phosphodiesterase) and IRA2 (encoding a GTPase activating protein- Ras-GAP, responsible for inactivating Ras-GTP) abolished glycolytic oscillations. CONCLUSIONS The genetic approach to characterising the glycolytic oscillations in yeast has demonstrated differential roles of the two types of subunits of PFK, and the isoforms of GAPDH and HK. Furthermore, it has shown that PDE2 and IRA2, encoding components of the cAMP pathway responsible for negative feedback regulation of PKA, are required for glycolytic oscillations, suggesting an enticing link between these cAMP pathway components and the glycolysis pathway enzymes shown to have the greatest role in glycolytic oscillation. This study suggests that a systematic genetic approach combined with mathematical modelling can advance the study of oscillatory phenomena.
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Affiliation(s)
- Thomas Williamson
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
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Qin J, Chai G, Brewer JM, Lovelace LL, Lebioda L. Structures of asymmetric complexes of human neuron specific enolase with resolved substrate and product and an analogous complex with two inhibitors indicate subunit interaction and inhibitor cooperativity. J Inorg Biochem 2012; 111:187-94. [PMID: 22437160 PMCID: PMC3371154 DOI: 10.1016/j.jinorgbio.2012.02.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 02/13/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
Abstract
In the presence of magnesium, enolase catalyzes the dehydration of 2-phospho-d-glycerate (PGA) to phosphoenolpyruvate (PEP) in glycolysis and the reverse reaction in gluconeogensis at comparable rates. The structure of human neuron specific enolase (hNSE) crystals soaked in PGA showed that the enzyme is active in the crystals and produced PEP; conversely soaking in PEP produced PGA. Moreover, the hNSE dimer contains PGA bound in one subunit and PEP or a mixture of PEP and PGA in the other. Crystals soaked in a mixture of competitive inhibitors tartronate semialdehyde phosphate (TSP) and lactic acid phosphate (LAP) showed asymmetry with TSP binding in the same site as PGA and LAP in the PEP site. Kinetic studies showed that the inhibition of NSE by mixtures of TSP and LAP is stronger than predicted for independently acting inhibitors. This indicates that in some cases inhibition of homodimeric enzymes by mixtures of inhibitors ("heteroinhibition") may offer advantages over single inhibitors.
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Affiliation(s)
- Jie Qin
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Geqing Chai
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC 29208
| | - John M. Brewer
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602
| | - Leslie L. Lovelace
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Lukasz Lebioda
- Department of Chemistry & Biochemistry, University of South Carolina, Columbia, SC 29208
- Center for Colon Cancer Research, University of South Carolina, Columbia, SC 29208
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Castillo-Romero A, Davids BJ, Lauwaet T, Gillin FD. Importance of enolase in Giardia lamblia differentiation. Mol Biochem Parasitol 2012; 184:122-5. [PMID: 22569588 DOI: 10.1016/j.molbiopara.2012.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/24/2012] [Accepted: 04/28/2012] [Indexed: 11/16/2022]
Abstract
The ability of Giardia to differentiate into cysts which survive in the environment and release the virulent trophozoites after ingestion in the small intestine is essential for transmission and disease. We examined the role of enolase, a glycolytic enzyme, in Giardia differentiation. The sequence of Giardia lamblia enolase (gEno) is most similar to enolases in Homo sapiens and Leishmania mexicana, and shows the conserved catalytic and metal-binding residues. We used an integration vector to stably express wild type and mutant gEno. In trophozoites, wild type gEno localized to the cell membrane, caudal flagella and cytosol. gEno is present on the wall of mature cysts, but not in encystation secretory vesicles (ESV). The expression of gEno with a deletion of residues G167-K169, or mutations H389Q/R390S significantly inhibited excystation while mutation of residue D257K had no effect. These results suggest a role for enolase in regulation of Giardia excystation.
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Moreno-Vargas LM, Carrillo-Ibarra N, Arzeta-Pino L, Benítez-Cardoza CG. Thermal unfolding of apo- and holo-enolase from Saccharomyces cerevisiae: Different mechanisms, similar activation enthalpies. Int J Biol Macromol 2011; 49:871-8. [DOI: 10.1016/j.ijbiomac.2011.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 07/24/2011] [Accepted: 07/28/2011] [Indexed: 10/17/2022]
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6
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Sánchez-Miguel DS, Romero-Jiménez J, Reyes-López CA, Cabrera-Ávila AL, Carrillo-Ibarra N, Benítez-Cardoza CG. Chemical Unfolding of Enolase from Saccharomyces cerevisiae Exhibits a Three-State Model. Protein J 2009; 29:1-10. [DOI: 10.1007/s10930-009-9215-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Zhao S, Choy BSF, Kornblatt MJ. Effects of the G376E and G157D mutations on the stability of yeast enolase--a model for human muscle enolase deficiency. FEBS J 2007; 275:97-106. [PMID: 18070103 DOI: 10.1111/j.1742-4658.2007.06177.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The first known human enolase deficiency was reported in 2001 [Comi GP, Fortunato F, Lucchiari S, Bordoni A, Prelle A, Jann S, Keller A, Ciscato P, Galbiati S, Chiveri L et al. (2001) Ann Neurol50, 202-207]. The subject had inherited two mutated genes for beta-enolase. These mutations changed glycine 156 to aspartate and glycine 374 to glutamate. In order to study the effects of these changes on the structure and stability of enolase, we have introduced the corresponding changes (G157D and G376E) into yeast enolase. The two variants are correctly folded. They are less stable than wild-type enolase with respect to thermal denaturation, and both have increased Kd values for subunit dissociation. At 37 degrees C, in the presence of salt, both are partially dissociated and are extensively cleaved by trypsin. Under the same conditions, wild-type enolase is fully dimeric and is only slightly cleaved by trypsin. However, wild-type enolase is also extensively cleaved if it is partially dissociated. The identification of the cleavage sites and spectral studies of enolase have revealed some of the structural differences between the dimeric and monomeric forms of this enzyme.
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Affiliation(s)
- Songping Zhao
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
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8
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De D, Dutta D, Kundu M, Mahato S, Schiavone MT, Chaudhuri S, Giri A, Gupta V, Bhattacharya SK. Inactive enzymatic mutant proteins (phosphoglycerate mutase and enolase) as sugar binders for ribulose-1,5-bisphosphate regeneration reactors. Microb Cell Fact 2005; 4:5. [PMID: 15689239 PMCID: PMC548675 DOI: 10.1186/1475-2859-4-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 02/02/2005] [Indexed: 11/12/2022] Open
Abstract
Background Carbon dioxide fixation bioprocess in reactors necessitates recycling of D-ribulose1,5-bisphosphate (RuBP) for continuous operation. A radically new close loop of RuBP regenerating reactor design has been proposed that will harbor enzyme-complexes instead of purified enzymes. These reactors will need binders enabling selective capture and release of sugar and intermediate metabolites enabling specific conversions during regeneration. In the current manuscript we describe properties of proteins that will act as potential binders in RuBP regeneration reactors. Results We demonstrate specific binding of 3-phosphoglycerate (3PGA) and 3-phosphoglyceraldehyde (3PGAL) from sugar mixtures by inactive mutant of yeast enzymes phosphoglycerate mutase and enolase. The reversibility in binding with respect to pH and EDTA has also been shown. No chemical conversion of incubated sugars or sugar intermediate metabolites were found by the inactive enzymatic proteins. The dissociation constants for sugar metabolites are in the micromolar range, both proteins showed lower dissociation constant (Kd) for 3-phosphoglycerate (655–796 μM) compared to 3-phosphoglyceraldehyde (822–966 μM) indicating higher affinity for 3PGA. The proteins did not show binding to glucose, sucrose or fructose within the sensitivity limits of detection. Phosphoglycerate mutase showed slightly lower stability on repeated use than enolase mutants. Conclusions The sugar and their intermediate metabolite binders may have a useful role in RuBP regeneration reactors. The reversibility of binding with respect to changes in physicochemical factors and stability when subjected to repeated changes in these conditions are expected to make the mutant proteins candidates for in-situ removal of sugar intermediate metabolites for forward driving of specific reactions in enzyme-complex reactors.
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Affiliation(s)
- Debojyoti De
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Debajyoti Dutta
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Moloy Kundu
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Sourav Mahato
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Marc T Schiavone
- Environmental Biotechnology Division, ABRD Company LLC, 1555 Wood Road, Cleveland, Ohio, 44121, USA
| | - Surabhi Chaudhuri
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Ashok Giri
- Plant Molecular Biology Division, National Chemical Laboratory, Pune 411008, India
| | - Vidya Gupta
- Plant Molecular Biology Division, National Chemical Laboratory, Pune 411008, India
| | - Sanjoy K Bhattacharya
- Department of Ophthalmic Research, Cleveland Clinic Foundation, Area I31, 9500 Euclid Avenue, Cleveland, Ohio, 44195, USA
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9
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Bartlett GJ, Borkakoti N, Thornton JM. Catalysing new reactions during evolution: economy of residues and mechanism. J Mol Biol 2003; 331:829-60. [PMID: 12909013 DOI: 10.1016/s0022-2836(03)00734-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diversity of function in some enzyme superfamilies shows that during evolution, enzymes have evolved to catalyse different reactions on the same structure scaffold. In this analysis, we examine in detail how enzymes can modify their chemistry, through a comparison of the catalytic residues and mechanisms in 27 pairs of homologous enzymes of totally different functions. We find that evolution is very economical. Enzymes retain structurally conserved residues to aid catalysis, including residues that bind catalytic metal ions and modulate cofactor chemistry. We examine the conservation of residue type and residue function in these structurally conserved residue pairs. Additionally, enzymes often retain common mechanistic steps catalyzed by structurally conserved residues. We have examined these steps in the context of their overall reactions.
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Affiliation(s)
- Gail J Bartlett
- Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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10
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Brewer JM, Glover CVC, Holland MJ, Lebioda L. Enzymatic function of loop movement in enolase: preparation and some properties of H159N, H159A, H159F, and N207A enolases. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:353-61. [PMID: 13678299 DOI: 10.1023/a:1025390123761] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The hypothesis that His159 in yeast enolase moves on a polypeptide loop to protonate the phosphoryl of 2-phosphoglycerate to initiate its conversion to phosphoenolpyruvate was tested by preparing H159N, H159A, and H159F enolases. These have 0.07%-0.25% of the native activity under standard assay conditions and the pH dependence of maximum velocities of H159A and H159N mutants is markedly altered. Activation by Mg2+ is biphasic, with the smaller Mg2+ activation constant closer to that of the "catalytic" Mg2+ binding site of native enolase and the larger in the mM range in which native enolase is inhibited. A third Mg2+ may bind to the phosphoryl, functionally replacing proton donation by His159. N207A enolase lacks an intersubunit interaction that stabilizes the closed loop(s) conformation when 2-phosphoglycerate binds. It has 21% of the native activity, also exhibits biphasic Mg2+ activation, and its reaction with the aldehyde analogue of the substrate is more strongly inhibited than is its normal enzymatic reaction. Polypeptide loop(s) closure may keep a proton from His159 interacting with the substrate phosphoryl oxygen long enough to stabilize a carbanion intermediate.
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Affiliation(s)
- John M Brewer
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
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11
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Poyner RR, Cleland WW, Reed GH. Role of metal ions in catalysis by enolase: an ordered kinetic mechanism for a single substrate enzyme. Biochemistry 2001; 40:8009-17. [PMID: 11434770 DOI: 10.1021/bi0103922] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spectroscopic and kinetic methods have been used to explore the roles of divalent metal ions in the enolase-catalyzed dehydration of 2-phosphoglycerate (2-PGA). Enolase requires 2 equiv of metal ion per active site for maximal activity. Previous crystallographic studies [Larsen, T. M., Wedekind, J. E., Rayment, I., and Reed, G. H. (1996) Biochemistry 35, 4349-4358] showed that both magnesium ions coordinated to the carboxylate group of the substrate/product-a scheme consistent with metal ion assistance in formation of the enolate intermediate. Electron paramagnetic resonance (EPR) data with 17O-labeled forms of phosphoenolpyruvate show that Mn(2+), bound at the lower affinity site, coordinates to one carboxylate oxygen and one phosphate oxygen of the substrate. These observations are fully consistent with the crystallographic data. Plots of activity versus log [metal ion] are bell-shaped, and the inhibitory phases of the profiles have been previously attributed to binding of metal ions at ancillary sites on the enzyme. However, the activation profiles and measurements of 2H kinetic isotope effects support an ordered kinetic mechanism wherein binding of 2-PGA precedes binding of the second metal ion, and release of the second metal ion occurs prior to departure of phosphoenolpyruvate. High concentrations of metal ion lead to inhibition in the ordered mechanism by interfering with product release. The 2H kinetic isotope effect is diminished in the inhibitory phases of the metal ion activation profiles in a manner that is consistent with the predominantly ordered mechanism. Zn(2+) gives lower maximal activity than Mg(2+), apparently due to slow release of Zn(2+) from the product complex. Addition of imidazole increases the maximal rate apparently by accelerating the release of Zn(2+) from the enzyme.
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Affiliation(s)
- R R Poyner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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12
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Hartleib J, Rüterjans H. Insights into the reaction mechanism of the diisopropyl fluorophosphatase from Loligo vulgaris by means of kinetic studies, chemical modification and site-directed mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1546:312-24. [PMID: 11295437 DOI: 10.1016/s0167-4838(01)00153-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic measurements, chemical modification and site-directed mutagenesis have been employed to gain deeper insights into the reaction mechanism of the diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris. Analysis of the kinetics of diisopropyl fluorophosphate hydrolysis reveals optimal enzyme activity at pH >/=8, 35 degrees C and an ionic strength of 500 mM NaCl, where k(cat) reaches a limiting value of 526 s(-1). The pH rate profile shows that full catalytic activity requires the deprotonation of an ionizable group with an apparent pK(a) of 6.82, DeltaH(ion) of 42 kJ/mol and DeltaS(ion) of 9.8 J/mol K at 25 degrees C. Chemical modification of aspartate, glutamate, cysteine, arginine, lysine and tyrosine residues indicates that these amino acids are not critical for catalysis. None of the six histidine residues present in DFPase reacts with diethyl pyrocarbonate (DEPC), suggesting that DEPC has no accessibility to the histidines. Therefore, all six histidine residues have been individually replaced by asparagine in order to identify residues participating in catalysis. Only substitution of H287 renders the enzyme catalytically almost inactive with a residual activity of approx. 4% compared to wild-type DFPase. The other histidine residues do not significantly influence the enzymatic activity, but H181 and H274 seem to have a stabilizing function. These results are indicative of a catalytic mechanism in which H287 acts as a general base catalyst activating a nucleophilic water molecule by the abstraction of a proton.
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Affiliation(s)
- J Hartleib
- Institute of Biophysical Chemistry, Johann Wolfgang Goethe University of Frankfurt/M., Marie-Curie-Strasse 9, 60439, Frankfurt/M., Germany
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13
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Brewer JM, Wampler JE. A differential scanning calorimetric study of the effects of metal ions, substrate/product, substrate analogues and chaotropic anions on the thermal denaturation of yeast enolase 1. Int J Biol Macromol 2001; 28:213-8. [PMID: 11251228 DOI: 10.1016/s0141-8130(00)00168-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The thermal denaturation of yeast enolase 1 was studied by differential scanning calorimetry (DSC) under conditions of subunit association/dissociation, enzymatic activity or substrate binding without turnover and substrate analogue binding. Subunit association stabilizes the enzyme, that is, the enzyme dissociates before denaturing. The conformational change produced by conformational metal ion binding increases thermal stability by reducing subunit dissociation. 'Substrate' or analogue binding additionally stabilizes the enzyme, irrespective of whether turnover is occurring, perhaps in part by the same mechanism. More strongly bound metal ions also stabilize the enzyme more, which we interpret as consistent with metal ion loss before denaturation, though possibly the denaturation pathway is different in the absence of metal ion. We suggest that some of the stabilization by 'substrate' and analogue binding is owing to the closure of moveable polypeptide loops about the active site, producing a more 'closed' and hence thermostable conformation.
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Affiliation(s)
- J M Brewer
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA
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14
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Brewer JM, Holland MJ, Lebioda L. The H159A mutant of yeast enolase 1 has significant activity. Biochem Biophys Res Commun 2000; 276:1199-202. [PMID: 11027610 DOI: 10.1006/bbrc.2000.3618] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The function of His159 in the enolase mechanism is disputed. Recently, Vinarov and Nowak (Biochemistry (1999) 38, 12138-12149) prepared the H159A mutant of yeast enolase 1 and expressed this in Escherichia coli. They reported minimal (ca. 0.01% of the native value) activity, though the protein appeared to be correctly folded, according to its CD spectrum, tryptophan fluorescence, and binding of metal ion and substrate. We prepared H159A enolase using a multicopy plasmid and expressed the enzyme in yeast. Our preparations of H159A enolase have 0.2-0.4% of the native activity under standard assay conditions and are further activated by Mg(2+) concentrations above 1 mM to 1-1.5% of the native activity. Native enolase 1 (and enolase 2) are inhibited by such Mg(2+) concentrations. It is possible that His159 is necessary for correct folding of the enzyme and that expression in E. coli leads to largely misfolded protein.
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Affiliation(s)
- J M Brewer
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA.
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15
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Kustrzeba-Wójcicka I, Golczak M. Enolase from Candida albicans--purification and characterization. Comp Biochem Physiol B Biochem Mol Biol 2000; 126:109-20. [PMID: 10825670 DOI: 10.1016/s0305-0491(00)00169-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper describes isolation of electrophoretically homogenous enolase from Candida albicans. The purification involved: disintegration of C. albicans cells in a Braun's mill (67-100%) ammonium sulfate precipitation, chromatography on DEAE-Sephadex A-50 at pH 9.0 and chromatography on CM-Sephadex A-50 at pH 6.2. The procedure resulted in a 30-fold purification of the enzyme with a recovery rate of 6% and a specific activity 35 U mg-1. The subunit molecular weight was 46 kDa and the pH optimum of the enzyme was 6.8. Km and Vmax values for the 2PGA-->PEP reaction were determined (Km = 0.95 mM, Vmax = 4200 mumol min-1 mumol-1). In the absence of orthophosphate, inhibition by fluoride was competitive, which became noncompetitive in the presence of phosphate. It was confirmed that Mg2+ is the most potent activator (Km = 0.286 mM); Mn2+ gave less activity and Zn2+ less still. It was also demonstrated that the presence of two types of cations in the reaction mixture nullified the activatory effect of the stronger agent. Properties of the enzyme from C. albicans are compared with those of enolases from other sources.
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Brewer JM, Glover CV, Holland MJ, Lebioda L. Significance of the enzymatic properties of yeast S39A enolase to the catalytic mechanism. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1383:351-5. [PMID: 9602170 DOI: 10.1016/s0167-4838(98)00004-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The S39A mutant of yeast enolase (isozyme 1), prepared by site-directed mutagenesis, has a relative Vmax of 0.01% and an activation constant for Mg2+ ca. 10-fold higher, compared with native enzyme. It is correctly folded. There is little effect of solvent viscosity on activity. We think that the loop Ser36-His43 fails to move to the 'closed' position upon catalytic Mg2+ binding, weakening several electrostatic interactions involved in the mechanism.
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Affiliation(s)
- J M Brewer
- Dept. of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA
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Zhang E, Brewer JM, Minor W, Carreira LA, Lebioda L. Mechanism of enolase: the crystal structure of asymmetric dimer enolase-2-phospho-D-glycerate/enolase-phosphoenolpyruvate at 2.0 A resolution. Biochemistry 1997; 36:12526-34. [PMID: 9376357 DOI: 10.1021/bi9712450] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Enolase, a glycolytic enzyme that catalyzes the dehydration of 2-phospho-d-glycerate (PGA) to form phosphoenolpyruvate (PEP), is a homodimer in all eukaryotes and many prokaryotes. Here, we report the crystal structure of a complex between yeast enolase and an equilibrium mixture of PGA and PEP. The structure has been refined using 29 854 reflections with an F/sigma(F) of >/=3 to an R of 0.137 with average deviations of bond lengths and bond angles from ideal values of 0.013 A and 3.1 degrees , respectively. In this structure, the dimer constitutes the crystallographic asymmetric unit. The two subunits are similar, and their superposition gives a rms distance between Calpha atoms of 0.91 A. The exceptions to this are the catalytic loop Val153-Phe169 where the atomic positions in the two subunits differ by up to 4 A and the loop Ser250-Gln277, which follows the catalytic loop Val153-Phe169. In the first subunit, the imidazole side chain of His159 is in contact with the phosphate group of the substrate/product molecule; in the other it is separated by water molecules. A series of hydrogen bonds leading to a neighboring enolase dimer can be identified as being responsible for ordering and stabilization of the conformationally different subunits in the crystal lattice. The electron density present in the active site suggests that in the active site with the direct ligand-His159 hydrogen bond PGA is predominantly bound while in the active site where water molecules separate His159 from the ligand the binding of PEP dominates. The structure indicates that the water molecule hydrating carbon-3 of PEP in the PEP --> PGA reaction is activated by the carboxylates of Glu168 and Glu211. The crystals are unique because they have resolved two intermediates on the opposite sides of the transition state.
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Affiliation(s)
- E Zhang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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