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Xu H, Yu B, Wei W, Chen X, Gao C, Liu J, Guo L, Song W, Liu L, Wu J. Improving tyrosol production efficiency through shortening the allosteric signal transmission distance of pyruvate decarboxylase. Appl Microbiol Biotechnol 2023; 107:3535-3549. [PMID: 37099057 DOI: 10.1007/s00253-023-12540-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/22/2023] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
Tyrosol is an important chemical in medicine and chemical industries, which can be synthesized by a four-enzyme cascade pathway constructed in our previous study. However, the low catalytic efficiency of pyruvate decarboxylase from Candida tropicalis (CtPDC) in this cascade is a rate-limiting step. In this study, we resolved the crystal structure of CtPDC and investigated the mechanism of allosteric substrate activation and decarboxylation of this enzyme toward 4-hydroxyphenylpyruvate (4-HPP). In addition, based on the molecular mechanism and structural dynamic changes, we conducted protein engineering of CtPDC to improve decarboxylation efficiency. The conversion of the best mutant, CtPDCQ112G/Q162H/G415S/I417V (CtPDCMu5), had over two-fold improvement compared to the wild-type. Molecular dynamic (MD) simulation revealed that the key catalytic distances and allosteric transmission pathways were shorter in CtPDCMu5 than in the wild type. Furthermore, when CtPDC in the tyrosol production cascade was replaced with CtPDCMu5, the tyrosol yield reached 38 g·L-1 with 99.6% conversion and 1.58 g·L-1·h-1 space-time yield in 24 h through further optimization of the conditions. Our study demonstrates that protein engineering of the rate-limiting enzyme in the tyrosol synthesis cascade provides an industrial-scale platform for the biocatalytic production of tyrosol. KEY POINTS: • Protein engineering of CtPDC based on allosteric regulation improved the catalytic efficiency of decarboxylation. • The application of the optimum mutant of CtPDC removed the rate-limiting bottleneck in the cascade. • The final titer of tyrosol reached 38 g·L-1 in 24 h in 3 L bioreactor.
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Affiliation(s)
- Huanhuan Xu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Bicheng Yu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China.
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2
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Zangelmi E, Ronda L, Castagna C, Campanini B, Veiga-da-Cunha M, Van Schaftingen E, Peracchi A. Off to a slow start: Analyzing lag phases and accelerating rates in steady-state enzyme kinetics. Anal Biochem 2020; 593:113595. [PMID: 31987861 DOI: 10.1016/j.ab.2020.113595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/10/2020] [Accepted: 01/20/2020] [Indexed: 10/25/2022]
Abstract
Steady-state enzyme kinetics typically relies on the measurement of 'initial rates', obtained when the substrate is not significantly consumed and the amount of product formed is negligible. Although initial rates are usually faster than those measured later in the reaction time-course, sometimes the speed of the reaction appears instead to increase with time, reaching a steady level only after an initial delay or 'lag phase'. This behavior needs to be interpreted by the experimentalists. To assist interpretation, this article analyzes the many reasons why, during an enzyme assay, the observed rate can be slow in the beginning and then progressively accelerate. The possible causes range from trivial artifacts to instances in which deeper mechanistic or biophysical factors are at play. We provide practical examples for most of these causes, based firstly on experiments conducted with ornithine δ-aminotransferase and with other pyridoxal-phosphate dependent enzymes that have been studied in our laboratory. On the side to this survey, we provide evidence that the product of the ornithine δ-aminotransferase reaction, glutamate 5-semialdehyde, cyclizes spontaneously to pyrroline 5-carboxylate with a rate constant greater than 3 s-1.
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Affiliation(s)
- Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43126, Parma, Italy
| | - Camilla Castagna
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Maria Veiga-da-Cunha
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200, Bruxelles, Belgium
| | - Emile Van Schaftingen
- De Duve Institute and WELBIO, UCLouvain, Avenue Hippocrate 75, 1200, Bruxelles, Belgium
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
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3
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Xu X, Wang C, Chen J, Yang S. Streptomyces virginiae PPDC Is a New Type of Phenylpyruvate Decarboxylase Composed of Two Subunits. ACS Chem Biol 2017; 12:2008-2014. [PMID: 28719183 DOI: 10.1021/acschembio.7b00307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomyces virginiae phenylpyruvate decarboxylase (PPDC) has not been identified before. Two putative branched-chain α-keto acid dehydrogenase subunit genes bkdC and bkdD from S. virginiae are similar to halves of other PPDC coding sequences. We cloned and characterized them biochemically in this work. The two proteins formed a stable complex attested by pull-down assay, consistent with the finding that their soluble expression was obtained only when they were coexpressed in Escherichia coli. The subunits were redesignated as SvPPDCα and SvPPDCβ, because the SvPPDCα/β complex catalyzed the conversion of phenylpyruvate to phenylacetaldehyde, reflecting the nature of the enzyme. Moreover, mutations of conserved residues in either of the two subunits led to inactivation or decreased specific activity of the enzymatic reaction. All previously identified PPDCs are encoded by a single gene. Here, we identified a new type of PPDC that contains two subunits, which gives new insights into the PPDC family.
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Affiliation(s)
- Xiaoshu Xu
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | | | - Sheng Yang
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing 210009, China
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4
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Pallitsch K, Rogers MP, Andrews FH, Hammerschmidt F, McLeish MJ. Phosphonodifluoropyruvate is a mechanism-based inhibitor of phosphonopyruvate decarboxylase from Bacteroides fragilis. Bioorg Med Chem 2017; 25:4368-4374. [PMID: 28693916 DOI: 10.1016/j.bmc.2017.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/11/2017] [Accepted: 06/12/2017] [Indexed: 10/19/2022]
Abstract
Bacteroides fragilis, a human pathogen, helps in the formation of intra-abdominal abscesses and is involved in 90% of anaerobic peritoneal infections. Phosphonopyruvate decarboxylase (PnPDC), a thiamin diphosphate (ThDP)-dependent enzyme, plays a key role in the formation of 2-aminoethylphosphonate, a component of the cell wall of B. fragilis. As such PnPDC is a possible target for therapeutic intervention in this, and other phosphonate producing organisms. However, the enzyme is of more general interest as it appears to be an evolutionary forerunner to the decarboxylase family of ThDP-dependent enzymes. To date, PnPDC has proved difficult to crystallize and no X-ray structures are available. In the past we have shown that ThDP-dependent enzymes will often crystallize if the cofactor has been irreversibly inactivated. To explore this possibility, and the utility of inhibitors of phosphonate biosynthesis as potential antibiotics, we synthesized phosphonodifluoropyruvate (PnDFP) as a prospective mechanism-based inhibitor of PnPDC. Here we provide evidence that PnDFP indeed inactivates the enzyme, that the inactivation is irreversible, and is accompanied by release of fluoride ion, i.e., PnDFP bears all the hallmarks of a mechanism-based inhibitor. Unfortunately, the enzyme remains refractive to crystallization.
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Affiliation(s)
| | - Megan P Rogers
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, USA
| | - Forest H Andrews
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, USA
| | | | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, USA.
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5
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Spinka M, Seiferheld S, Zimmermann P, Bergner E, Blume AK, Schierhorn A, Reichenbach T, Pertermann R, Ehrt C, König S. Significance of Individual Residues at the Regulatory Site of Yeast Pyruvate Decarboxylase for Allosteric Substrate Activation. Biochemistry 2017; 56:1285-1298. [PMID: 28170226 DOI: 10.1021/acs.biochem.6b01158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalytic activity of the allosteric enzyme pyruvate decarboxylase from yeast is strictly controlled by its own substrate pyruvate via covalent binding at a separate regulatory site. Kinetic studies, chemical modifications, cross-linking, small-angle X-ray scattering, and crystal structure analyses have led to a detailed understanding of the substrate activation mechanism at an atomic level with C221 as the core moiety of the regulatory site. To characterize the individual role of the residues adjacent to C221, we generated variants H92F, H225F, H310F, A287G, S311A, and C221A/C222A. The integrity of the protein structure of the variants was established by small-angle X-ray scattering measurements. The analyses of both steady state and transient kinetic data allowed the identification of the individual roles of the exchanged side chains during allosteric enzyme activation. In each case, the kinetic pattern of activation was modulated but not completely abolished. Despite the crucial role of C221, the covalent binding of pyruvate is not obligate for enzyme activation but is a requirement for a kinetically efficient transition from the inactive to the active state. Moreover, only one of the three histidines guiding the activator molecule to the binding pocket, H310, specifically interacts with C221. H310 stabilizes the thiolate form of C221, ensuring a rapid nucleophilic attack of the thiolate sulfur on C2 of the regulatory pyruvate, thus forming a regulatory dyad. The influence of the other two histidines is less pronounced. Substrate activation is slightly weakened for A287G and significantly retarded for S311A.
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Affiliation(s)
- Michael Spinka
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Sebastian Seiferheld
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Philipp Zimmermann
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Elena Bergner
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Anne-Kathrin Blume
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Angelika Schierhorn
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Tom Reichenbach
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Robert Pertermann
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Christiane Ehrt
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
| | - Stephan König
- Department for Enzymology, Institute of Biochemistry & Biotechnology, Faculty of Biosciences, Martin-Luther-University Halle-Wittenberg , 06120 Halle (Saale), Germany
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6
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Single-Step Partial Purification of Intracellular β-Galactosidase from Kluyveromyces lactis Using Microemulsion Droplets. Appl Biochem Biotechnol 2016; 180:1000-1015. [DOI: 10.1007/s12010-016-2148-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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7
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Agarwal PK, Uppada V, Noronha SB. Comparison of pyruvate decarboxylases from Saccharomyces cerevisiae and Komagataella pastoris (Pichia pastoris). Appl Microbiol Biotechnol 2013; 97:9439-49. [DOI: 10.1007/s00253-013-4758-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/03/2013] [Accepted: 02/05/2013] [Indexed: 11/30/2022]
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8
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Kinetic and thermodynamic characterization of the functional properties of a hybrid versatile peroxidase using isothermal titration calorimetry: Insight into manganese peroxidase activation and lignin peroxidase inhibition. Biochimie 2012; 94:1221-31. [PMID: 22586704 DOI: 10.1016/j.biochi.2012.02.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Isothermal titration calorimetry (ITC) was developed for measuring lignin peroxidase (LiP) and manganese peroxidase (MnP) activities of versatile peroxidase (VP) from Bjerkandera adusta. Developing an ITC approach provided an alternative to colorimetric methods that enabled reaction kinetics to be accurately determined. Although VP from Bjerkandera adjusta is a hybrid enzyme, specific conditions of [Mn+2] and pH were defined that limited activity to either LiP or MnP activities, or enabled both to be active simultaneously. MnP activity was found to be more efficient than LiP activity, with activity increasing with increasing concentrations of Mn+2. These properties of MnP were explained by a second metal binding site involved in homotropic substrate (Mn+2) activation. The activation of MnP was also accompanied by a decrease in both activation energy and substrate (Mn) affinity, reflecting a flexible enzyme structure. In contrast to MnP activity, LiP activity was inhibited by high dye (substrate) concentrations arising from uncompetitive substrate inhibition caused by substrate binding to a site distinct from the catalytic site. Our study provides a new level of understanding about the mechanism of substrate regulation of catalysis in VP from B. adjusta, providing insight into a class of enzyme, hybrid class II peroxidases, for which little experimental data is available.
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9
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Hüttl S, Fiebig J, Kutter S, Hause G, Lilie H, Spinka M, König S. Catalytically active filaments - pyruvate decarboxylase from Neurospora crassa. pH-controlled oligomer structure and catalytic function. FEBS J 2011; 279:275-84. [PMID: 22077835 DOI: 10.1111/j.1742-4658.2011.08421.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Pyruvate decarboxylase is a key enzyme in organisms whose energy metabolism is based on alcoholic fermentation. The enzyme catalyses the nonoxidative decarboxylation of 2-oxo acids in the presence of the cofactors thiamine diphosphate and magnesium ions. Pyruvate decarboxylase species from yeasts and plant seeds studied to date are allosterically activated by their substrate pyruvate. However, detailed kinetic studies on the enzyme from Neurospora crassa demonstrate for the first time the lack of substrate activation for a yeast pyruvate decarboxylase species. The quaternary structure of this enzyme species is also peculiar because it forms filamentous structures. The complex enzyme structure was analysed using a number of methods, including small-angle X-ray solution scattering, transmission electron microscopy, analytical ultracentrifugation and size-exclusion chromatography. These measurements were complemented by detailed kinetic studies in dependence on the pH.
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Affiliation(s)
- Stefanie Hüttl
- Division of Enzymology, Institute of Biochemistry & Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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10
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Fedorov DN, Doronina NV, Trotsenko YA. Cloning and characterization of indolepyruvate decarboxylase from Methylobacterium extorquens AM1. BIOCHEMISTRY (MOSCOW) 2011; 75:1435-43. [PMID: 21314613 DOI: 10.1134/s0006297910120035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
For the first time for methylotrophic bacteria an enzyme of phytohormone indole-3-acetic acid (IAA) biosynthesis, indole-3-pyruvate decarboxylase (EC 4.1.1.74), has been found. An open reading frame (ORF) was identified in the genome of facultative methylotroph Methylobacterium extorquens AM1 using BLAST. This ORF encodes thiamine diphosphate-dependent 2-keto acid decarboxylase and has similarity with indole-3-pyruvate decarboxylases, which are key enzymes of IAA biosynthesis. The ORF of the gene, named ipdC, was cloned into overexpression vector pET-22b(+). Recombinant enzyme IpdC was purified from Escherichia coli BL21(DE3) and characterized. The enzyme showed the highest k(cat) value for benzoylformate, albeit the indolepyruvate was decarboxylated with the highest catalytic efficiency (k(cat)/K(m)). The molecular mass of the holoenzyme determined using gel-permeation chromatography corresponds to a 245-kDa homotetramer. An ipdC-knockout mutant of M. extorquens grown in the presence of tryptophan had decreased IAA level (46% of wild type strain). Complementation of the mutation resulted in 6.3-fold increase of IAA concentration in the culture medium compared to that of the mutant strain. Thus involvement of IpdC in IAA biosynthesis in M. extorquens was shown.
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Affiliation(s)
- D N Fedorov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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11
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König S, Spinka M, Kutter S. Allosteric activation of pyruvate decarboxylases. A never-ending story? ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2009.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Kutter S, Weiss MS, Wille G, Golbik R, Spinka M, König S. Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation. J Biol Chem 2009; 284:12136-44. [PMID: 19246454 PMCID: PMC2673282 DOI: 10.1074/jbc.m806228200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 02/17/2009] [Indexed: 11/06/2022] Open
Abstract
The mechanism by which the enzyme pyruvate decarboxylase from two yeast species is activated allosterically has been elucidated. A total of seven three-dimensional structures of the enzyme, of enzyme variants, or of enzyme complexes from two yeast species, three of them reported here for the first time, provide detailed atomic resolution snapshots along the activation coordinate. The prime event is the covalent binding of the substrate pyruvate to the side chain of cysteine 221, thus forming a thiohemiketal. This reaction causes the shift of a neighboring amino acid, which eventually leads to the rigidification of two otherwise flexible loops, one of which provides two histidine residues necessary to complete the enzymatically competent active site architecture. The structural data are complemented and supported by kinetic investigations and binding studies, providing a consistent picture of the structural changes occurring upon enzyme activation.
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Affiliation(s)
- Steffen Kutter
- Institute for Biochemistry and Biotechnology, Faculty of Biological Sciences, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
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13
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Taylor M, Tuffin M, Burton S, Eley K, Cowan D. Microbial responses to solvent and alcohol stress. Biotechnol J 2008; 3:1388-97. [PMID: 18956369 DOI: 10.1002/biot.200800158] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mark Taylor
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Cape Town, South Africa
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14
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Kutter S, Spinka M, Koch MHJ, König S. The influence of protein concentration on oligomer structure and catalytic function of two pyruvate decarboxylases. Protein J 2008; 26:585-91. [PMID: 17805949 DOI: 10.1007/s10930-007-9101-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
As a general rule protein concentration typical for structural studies differs considerably from that chosen for kinetic investigations. Consequently, structure-function relationships are often postulated without appropriate knowledge, whether the functional behaviour of the enzyme is the same in both protein concentration ranges. To deal with this question, substrate activation kinetics of two well-characterised yeast pyruvate decarboxylases, from Saccharomyces cerevisiae and from Kluyveromyces lactis, were analysed over the broad protein concentration range 2-2,000 microg/mL. Analytical ultracentrifugation and small-angle X-ray scattering were used to analyse the enzymes' oligomer structure in aqueous solution. For the upper part of the concentration range the determined parameters, like catalytic activity, observed substrate activation rates, sedimentation coefficients and scattering parameters are independent on enzyme concentration changes. No indication of protein aggregation is detectable. However, significant changes occur at low enzyme concentration. The catalytically active tetramer dissociates progressively into dimers with comparable catalytic activity, but with significantly accelerated substrate activation.
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Affiliation(s)
- Steffen Kutter
- Institute for Biochemistry & Biotechnology, Faculty for Life Sciences, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halles (Saale), Germany
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15
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Werther T, Spinka M, Tittmann K, Schütz A, Golbik R, Mrestani-Klaus C, Hübner G, König S. Amino acids allosterically regulate the thiamine diphosphate-dependent alpha-keto acid decarboxylase from Mycobacterium tuberculosis. J Biol Chem 2007; 283:5344-54. [PMID: 18086676 DOI: 10.1074/jbc.m706569200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gene rv0853c from Mycobacterium tuberculosis strain H37Rv codes for a thiamine diphosphate-dependent alpha-keto acid decarboxylase (MtKDC), an enzyme involved in the amino acid degradation via the Ehrlich pathway. Steady state kinetic experiments were performed to determine the substrate specificity of MtKDC. The mycobacterial enzyme was found to convert a broad spectrum of branched-chain and aromatic alpha-keto acids. Stopped-flow kinetics showed that MtKDC is allosterically activated by alpha-keto acids. Even more, we demonstrate that also amino acids are potent activators of this thiamine diphosphate-dependent enzyme. Thus, metabolic flow through the Ehrlich pathway can be directly regulated at the decarboxylation step. The influence of amino acids on MtKDC catalysis was investigated, and implications for other thiamine diphosphate-dependent enzymes are discussed.
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Affiliation(s)
- Tobias Werther
- Institute of Biochemistry and Biotechnology, Faculty for Biological Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle Saale, Germany
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16
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Versées W, Spaepen S, Wood MDH, Leeper FJ, Vanderleyden J, Steyaert J. Molecular Mechanism of Allosteric Substrate Activation in a Thiamine Diphosphate-dependent Decarboxylase. J Biol Chem 2007; 282:35269-78. [PMID: 17905741 DOI: 10.1074/jbc.m706048200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.
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Affiliation(s)
- Wim Versées
- Department of Ultrastructure, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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17
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Spaepen S, Versées W, Gocke D, Pohl M, Steyaert J, Vanderleyden J. Characterization of phenylpyruvate decarboxylase, involved in auxin production of Azospirillum brasilense. J Bacteriol 2007; 189:7626-33. [PMID: 17766418 PMCID: PMC2168738 DOI: 10.1128/jb.00830-07] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Azospirillum brasilense belongs to the plant growth-promoting rhizobacteria with direct growth promotion through the production of the phytohormone indole-3-acetic acid (IAA). A key gene in the production of IAA, annotated as indole-3-pyruvate decarboxylase (ipdC), has been isolated from A. brasilense, and its regulation was reported previously (A. Vande Broek, P. Gysegom, O. Ona, N. Hendrickx, E. Prinsen, J. Van Impe, and J. Vanderleyden, Mol. Plant-Microbe Interact. 18:311-323, 2005). An ipdC-knockout mutant was found to produce only 10% (wt/vol) of the wild-type IAA production level. In this study, the encoded enzyme is characterized via a biochemical and phylogenetic analysis. Therefore, the recombinant enzyme was expressed and purified via heterologous overexpression in Escherichia coli and subsequent affinity chromatography. The molecular mass of the holoenzyme was determined by size-exclusion chromatography, suggesting a tetrameric structure, which is typical for 2-keto acid decarboxylases. The enzyme shows the highest kcat value for phenylpyruvate. Comparing values for the specificity constant kcat/Km, indole-3-pyruvate is converted 10-fold less efficiently, while no activity could be detected with benzoylformate. The enzyme shows pronounced substrate activation with indole-3-pyruvate and some other aromatic substrates, while for phenylpyruvate it appears to obey classical Michaelis-Menten kinetics. Based on these data, we propose a reclassification of the ipdC gene product of A. brasilense as a phenylpyruvate decarboxylase (EC 4.1.1.43).
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Affiliation(s)
- Stijn Spaepen
- Centre of Microbial and Plant Genetics, K.U. Leuven, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
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Versées W, Spaepen S, Vanderleyden J, Steyaert J. The crystal structure of phenylpyruvate decarboxylase from Azospirillum brasilense at 1.5 Å resolution. FEBS J 2007; 274:2363-75. [PMID: 17403037 DOI: 10.1111/j.1742-4658.2007.05771.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenylpyruvate decarboxylase (PPDC) of Azospirillum brasilense, involved in the biosynthesis of the plant hormone indole-3-acetic acid and the antimicrobial compound phenylacetic acid, is a thiamine diphosphate-dependent enzyme that catalyses the nonoxidative decarboxylation of indole- and phenylpyruvate. Analogous to yeast pyruvate decarboxylases, PPDC is subject to allosteric substrate activation, showing sigmoidal v versus [S] plots. The present paper reports the crystal structure of this enzyme determined at 1.5 A resolution. The subunit architecture of PPDC is characteristic for other members of the pyruvate oxidase family, with each subunit consisting of three domains with an open alpha/beta topology. An active site loop, bearing the catalytic residues His112 and His113, could not be modelled due to flexibility. The biological tetramer is best described as an asymmetric dimer of dimers. A cysteine residue that has been suggested as the site for regulatory substrate binding in yeast pyruvate decarboxylase is not conserved, requiring a different mechanism for allosteric substrate activation in PPDC. Only minor changes occur in the interactions with the cofactors, thiamine diphosphate and Mg2+, compared to pyruvate decarboxylase. A greater diversity is observed in the substrate binding pocket accounting for the difference in substrate specificity. Moreover, a catalytically important glutamate residue conserved in nearly all decarboxylases is replaced by a leucine in PPDC. The consequences of these differences in terms of the catalytic and regulatory mechanism of PPDC are discussed.
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Affiliation(s)
- Wim Versées
- Department of Ultrastructure, Vrije Universiteit Brussel, Brussels, Belgium.
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19
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Purification and characterisation of two isozymes of pyruvate decarboxylase from Rhizopus oryzae. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2006.05.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Joseph E, Wei W, Tittmann K, Jordan F. Function of a conserved loop of the beta-domain, not involved in thiamin diphosphate binding, in catalysis and substrate activation in yeast pyruvate decarboxylase. Biochemistry 2007; 45:13517-27. [PMID: 17087505 DOI: 10.1021/bi0615588] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The X-ray crystal structure of pyruvamide-activated yeast pyruvate decarboxylase (YPDC) revealed a flexible loop spanning residues 290 to 304 on the beta-domain of the enzyme, not seen in the absence of pyruvamide, a substrate activator surrogate. Site-directed mutagenesis studies revealed that residues on the loop affect the activity, with some residues reducing k(cat)/K(m) by at least 1000-fold. In the pyruvamide-activated form, the loop located on the beta domain can transfer information to the active center thiamin diphosphate (ThDP) located at the interface of the alpha and gamma domains. The sigmoidal v(0)-[S] curve with wild-type YPDC attributed to substrate activation is modulated for most variants, but is not abolished. Pre-steady-state stopped-flow studies for product formation on these loop variants provided evidence for three enzyme conformations connected by two transitions, as already noted for the wild-type YPDC at pH 5.0 [Sergienko, E. A., and Jordan, F. (2002) Biochemistry 41, 3952-3967]. (1)H NMR analysis of the intermediate distribution resulting from acid quench [Tittmann et al. (2003) Biochemistry 42, 7885-7891] with all YPDC variants indicated that product release is rate limiting in the steady state. Apparently, the loop is not solely responsible for the substrate activation behavior, rather it may affect the behavior of residue C221 identified as the trigger for substrate activation. The most important function of the loop is to control the conformational equilibrium between the "open" and "closed" conformations of the enzyme identified in the pyruvamide-activated structure [Lu et al. (2000) Eur. J. Biochem. 267, 861-868].
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Affiliation(s)
- Ebenezer Joseph
- Department of Chemistry, Rutgers, the State University of New Jersey, Newark, New Jersey 07102, USA
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21
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Yep A, Kenyon GL, McLeish MJ. Determinants of substrate specificity in KdcA, a thiamin diphosphate-dependent decarboxylase. Bioorg Chem 2006; 34:325-36. [PMID: 17028071 DOI: 10.1016/j.bioorg.2006.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 08/16/2006] [Accepted: 08/19/2006] [Indexed: 11/26/2022]
Abstract
Thiamin diphosphate-dependent decarboxylases catalyze the non-oxidative decarboxylation of 2-keto carboxylic acids. Although they display relatively low sequence similarity, and broadly different range of substrates, these enzymes show a common homotetrameric structure. Here we describe a kinetic characterization of the substrate spectrum of a recently identified member of this class, the branched chain 2-keto acid decarboxylase (KdcA) from Lactococcus lactis. In order to understand the structural basis for KdcA substrate recognition we developed a homology model of its structure. Ser286, Phe381, Val461 and Met358 were identified as residues that appeared to shape the substrate binding pocket. Subsequently, site-directed mutagenesis was carried out on these residues with a view to converting KdcA into a pyruvate decarboxylase. The results show that the mutations all lowered the Km value for pyruvate and both the S286Y and F381W variants also had greatly increased values of k(cat) with pyruvate as a substrate.
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Affiliation(s)
- Alejandra Yep
- College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA
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Kutter S, Wille G, Relle S, Weiss MS, Hübner G, König S. The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme. FEBS J 2006; 273:4199-209. [PMID: 16939618 DOI: 10.1111/j.1742-4658.2006.05415.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis has been determined to 2.26 A resolution. Like other yeast enzymes, Kluyveromyces lactis pyruvate decarboxylase is subject to allosteric substrate activation. Binding of substrate at a regulatory site induces catalytic activity. This process is accompanied by conformational changes and subunit rearrangements. In the nonactivated form of the corresponding enzyme from Saccharomyces cerevisiae, all active sites are solvent accessible due to the high flexibility of loop regions 106-113 and 292-301. The binding of the activator pyruvamide arrests these loops. Consequently, two of four active sites become closed. In Kluyveromyces lactis pyruvate decarboxylase, this half-side closed tetramer is present even without any activator. However, one of the loops (residues 105-113), which are flexible in nonactivated Saccharomyces cerevisiae pyruvate decarboxylase, remains flexible. Even though the tetramer assemblies of both enzyme species are different in the absence of activating agents, their substrate activation kinetics are similar. This implies an equilibrium between the open and the half-side closed state of yeast pyruvate decarboxylase tetramers. The completely open enzyme state is favoured for Saccharomyces cerevisiae pyruvate decarboxylase, whereas the half-side closed form is predominant for Kluyveromyces lactis pyruvate decarboxylase. Consequently, the structuring of the flexible loop region 105-113 seems to be the crucial step during the substrate activation process of Kluyveromyces lactis pyruvate decarboxylase.
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Affiliation(s)
- Steffen Kutter
- Institute for Biochemistry, Department of Biochemistry & Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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Affiliation(s)
- Ray Fall
- Department of Chemistry and Biochemistry, and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309-0215, USA.
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Schütz A, Golbik R, Tittmann K, Svergun DI, Koch MHJ, Hübner G, König S. Studies on structure-function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:2322-31. [PMID: 12752452 DOI: 10.1046/j.1432-1033.2003.03602.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Enterobacter cloacae, isolated from the rhizosphere of cucumbers, produces large amounts of indole-3-acetic acid. Indolepyruvate decarboxylase, the key enzyme in the biosynthetic pathway of indole-3-acetic acid, catalyses the formation of indole-3-acetaldehyde and carbon dioxide from indole-3-pyruvic acid. The enzyme requires the cofactors thiamine diphosphate and magnesium ions for catalytic activity. Recombinant indolepyruvate decarboxylase was purified from the host Escherichia coli strain JM109. Specificity of the enzyme for the substrates indole-3-pyruvic acid, pyruvic acid, benzoylformic acid, and seven benzoylformic acid analogues was investigated using a continuous optical assay. Stopped-flow kinetic data showed no indication for substrate activation in the decarboxylation reaction of indole-3-pyruvic acid, pyruvic acid or benzoylformic acid. Size exclusion chromatography and small angle X-ray solution scattering experiments suggested the tetramer as the catalytically active state and a pH-dependent subunit association equilibrium. Analysis of the kinetic constants of the benzoylformic acid analogues according to Hansch et al. [Hansch, C., Leo, A., Unger, S.H., Kim, K.H., Nikaitani, D & Lien, E.J. (1973) J. Med. Chem.16, 1207-1216] and comparison with indole-3-pyruvic acid conversion by pyruvate decarboxylases from Saccharomyces cerevisiae and Zymomonas mobilis provided some insight into the catalytic mechanism of indolepyruvate decarboxylase.
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Affiliation(s)
- Anja Schütz
- Institut für Biochemie, Fachbereich Biochemie/Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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Current awareness on yeast. Yeast 2002; 19:1373-80. [PMID: 12526113 DOI: 10.1002/yea.830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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