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Rodrigues MJ, Giri N, Royant A, Zhang Y, Bolton R, Evans G, Ealick SE, Begley T, Tews I. Trapping and structural characterisation of a covalent intermediate in vitamin B6 biosynthesis catalysed by the Pdx1 PLP synthase. RSC Chem Biol 2022; 3:227-230. [PMID: 35360887 PMCID: PMC8827014 DOI: 10.1039/d1cb00160d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 12/01/2022] Open
Abstract
The Pdx1 enzyme catalyses condensation of two carbohydrates and ammonia to form pyridoxal 5-phosphate (PLP) via an imine relay mechanism of carbonyl intermediates. The I333 intermediate characterised here using structural, UV-vis absorption spectroscopy and mass spectrometry analyses rationalises stereoselective deprotonation and subsequent substrate assisted phosphate elimination, central to PLP biosynthesis. Explaining stereoselective deprotonation and phosphate elimination in PLP biosynthesis through crystal structure, UV-vis absorption spectroscopic and mass spectrometric characterisation of a chromophoric intermediate.![]()
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Affiliation(s)
- Matthew J. Rodrigues
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Nitai Giri
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Antoine Royant
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), CS 10090, Grenoble Cedex 9 38044, France
- European Synchrotron Radiation Facility, CS 40220, Grenoble Cedex 9 38043, France
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Rachel Bolton
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Steve E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Tadhg Begley
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Ivo Tews
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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2
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Evers MS, Roullier-Gall C, Morge C, Sparrow C, Gobert A, Alexandre H. Vitamins in wine: Which, what for, and how much? Compr Rev Food Sci Food Saf 2021; 20:2991-3035. [PMID: 33884746 DOI: 10.1111/1541-4337.12743] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/11/2021] [Accepted: 03/01/2021] [Indexed: 12/01/2022]
Abstract
Vitamins are essential compounds to yeasts, and notably in winemaking contexts. Vitamins are involved in numerous yeast metabolic pathways, including those of amino acids, fatty acids, and alcohols, which suggests their notable implication in fermentation courses, as well as in the development of aromatic compounds in wines. Although they are major components in the course of those microbial processes, their significance and impact have not been extensively studied in the context of winemaking and wine products, as most of the studies focusing on the subject in the past decades have relied on relatively insensitive and imprecise analytical methods. Therefore, this review provides an extensive overview of the current knowledge regarding the impacts of vitamins on grape must fermentations, wine-related yeast metabolisms, and requirements, as well as on the profile of wine sensory characteristics. We also highlight the methodologies and techniques developed over time to perform vitamin analysis in wines, and assess the importance of precisely defining the role played by vitamins in winemaking processes, to ensure finer control of the fermentation courses and product characteristics in a highly complex matrix.
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Affiliation(s)
- Marie Sarah Evers
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France.,SAS Sofralab, Magenta, France
| | - Chloé Roullier-Gall
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
| | | | | | | | - Hervé Alexandre
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, Dijon, France
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3
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Labuschagne P, Divol B. Thiamine: a key nutrient for yeasts during wine alcoholic fermentation. Appl Microbiol Biotechnol 2021; 105:953-973. [PMID: 33404836 DOI: 10.1007/s00253-020-11080-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 12/27/2020] [Indexed: 12/27/2022]
Abstract
Alcoholic fermentation is a crucial step of winemaking, during which yeasts convert sugars to alcohol and also produce or biotransform numerous flavour compounds. In this context, nutrients are essential compounds to support yeast growth and ultimately ensure complete fermentation, as well as optimized production of flavour compounds over that of off-flavour compounds. In particular, the vitamin thiamine not only plays an essential cofactor role for several enzymes involved in various metabolic pathways, including those leading to the production of wine-relevant flavour compounds, but also aids yeast survival via thiamine-dependent stress protection functions. Most yeast species are able to both assimilate exogenous thiamine into the cell and synthesize thiamine de novo. However, the mechanism and level of thiamine accumulation depend on several factors. This review provides an in-depth overview of thiamine utilization and metabolism in the model yeast species Saccharomyces cerevisiae, as well as the current knowledge on (1) the intracellular functions of thiamine, (2) the balance between and regulation of uptake and synthesis of thiamine and (3) the multitude of factors influencing thiamine availability and utilization. For the latter, a particular emphasis is placed on conditions occurring during wine fermentation. The adequacy of thiamine concentration in grape must to ensure successful fermentation is discussed together with the effect of thiamine concentration on fermentation kinetics and on wine sensory properties. This knowledge may serve as a resource to optimise thiamine concentrations for optimal industrial application of yeasts. KEY POINTS: • Thiamine uptake is preferred over biosynthesis and is transcriptionally repressed. • Multiple factors affect thiamine synthesis, availability and uptake for wine yeast. • Thiamine availability impacts fermentation kinetics and wine's sensory properties.
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Affiliation(s)
- Pwj Labuschagne
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Private Bag X1, Matieland, 7602, South Africa
| | - B Divol
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Private Bag X1, Matieland, 7602, South Africa.
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4
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Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
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Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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5
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Robinson GC, Kaufmann M, Roux C, Martinez-Font J, Hothorn M, Thore S, Fitzpatrick TB. Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3: a total eclipse. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:400-415. [PMID: 30988257 DOI: 10.1107/s2059798319002912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022]
Abstract
Pseudoenzymes have burst into the limelight recently as they provide another dimension to regulation of cellular protein activity. In the eudicot plant lineage, the pseudoenzyme PDX1.2 and its cognate enzyme PDX1.3 interact to regulate vitamin B6 biosynthesis. This partnership is important for plant fitness during environmental stress, in particular heat stress. PDX1.2 increases the catalytic activity of PDX1.3, with an overall increase in vitamin B6 biosynthesis. However, the mechanism by which this is achieved is not known. In this study, the Arabidopsis thaliana PDX1.2-PDX1.3 complex was crystallized in the absence and presence of ligands, and attempts were made to solve the X-ray structures. Three PDX1.2-PDX1.3 complex structures are presented: the PDX1.2-PDX1.3 complex as isolated, PDX1.2-PDX1.3-intermediate (in the presence of substrates) and a catalytically inactive complex, PDX1.2-PDX1.3-K97A. Data were also collected from a crystal of a selenomethionine-substituted complex, PDX1.2-PDX1.3-SeMet. In all cases the protein complexes assemble as dodecamers, similar to the recently reported individual PDX1.3 homomer. Intriguingly, the crystals of the protein complex are statistically disordered owing to the high degree of structural similarity of the individual PDX1 proteins, such that the resulting configuration is a composite of both proteins. Despite the differential methionine content, selenomethionine substitution of the PDX1.2-PDX1.3 complex did not resolve the problem. Furthermore, a comparison of the catalytically competent complex with a noncatalytic complex did not facilitate the resolution of the individual proteins. Interestingly, another catalytic lysine in PDX1.3 (Lys165) that pivots between the two active sites in PDX1 (P1 and P2), and the corresponding glutamine (Gln169) in PDX1.2, point towards P1, which is distinctive to the initial priming for catalytic action. This state was previously only observed upon trapping PDX1.3 in a catalytically operational state, as Lys165 points towards P2 in the resting state. Overall, the study shows that the integration of PDX1.2 into a heteromeric dodecamer assembly with PDX1.3 does not cause a major structural deviation from the overall architecture of the homomeric complex. Nonetheless, the structure of the PDX1.2-PDX1.3 complex highlights enhanced flexibility in key catalytic regions for the initial steps of vitamin B6 biosynthesis. This report highlights what may be an intrinsic limitation of X-ray crystallography in the structural investigation of pseudoenzymes.
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Affiliation(s)
- Graham C Robinson
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Markus Kaufmann
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Céline Roux
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Jacobo Martinez-Font
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Michael Hothorn
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland
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6
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Vazquez-Hernandez C, Loza A, Peguero-Sanchez E, Segovia L, Gutierrez-Rios RM. Identification of reaction organization patterns that naturally cluster enzymatic transformations. BMC SYSTEMS BIOLOGY 2018; 12:63. [PMID: 29848336 PMCID: PMC5977463 DOI: 10.1186/s12918-018-0583-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/09/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Metabolic reactions are chemical transformations commonly catalyzed by enzymes. In recent years, the explosion of genomic data and individual experimental characterizations have contributed to the construction of databases and methodologies for the analysis of metabolic networks. Some methodologies based on graph theory organize compound networks into metabolic functional categories without preserving biochemical pathways. Other methods based on chemical group exchange and atom flow trace the conversion of substrates into products in detail, which is useful for inferring metabolic pathways. METHODS Here, we present a novel rule-based approach incorporating both methods that decomposes each reaction into architectures of compound pairs and loner compounds that can be organized into tree structures. We compared the tree structure-compound pairs to those reported in the KEGG-RPAIR dataset and obtained a match precision of 81%. The generated tree structures naturally clustered all reactions into general reaction patterns of compounds with similar chemical transformations. The match precision of each cluster was calculated and used to suggest reactant-pairs for which manual curation can be avoided because this is the main goal of the method. We evaluated catalytic processes in the clusters based on Enzyme Commission categories that revealed preferential use of enzyme classes. CONCLUSIONS We demonstrate that the application of simple rules can enable the identification of reaction patterns reflecting metabolic reactions that transform substrates into products and the types of catalysis involved in these transformations. Our rule-based approach can be incorporated as the input in pathfinders or as a tool for the construction of reaction classifiers, indicating its usefulness for predicting enzyme catalysis.
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Affiliation(s)
- Carlos Vazquez-Hernandez
- Departamento de Microbiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Apdo, Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Antonio Loza
- Departamento de Microbiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Apdo, Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Esteban Peguero-Sanchez
- Departamento de Microbiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Apdo, Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Lorenzo Segovia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología Universidad Nacional Autónoma de México, Apdo, Postal 510-3, 62250, Cuernavaca, Morelos, Mexico
| | - Rosa-Maria Gutierrez-Rios
- Departamento de Microbiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Apdo, Postal 510-3, 62250, Cuernavaca, Morelos, Mexico.
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7
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Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017; 7:138-146. [PMID: 28355531 PMCID: PMC5376308 DOI: 10.1016/j.ijpddr.2017.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/28/2017] [Accepted: 03/20/2017] [Indexed: 11/24/2022]
Abstract
Chloroquine, long the default first-line treatment against malaria, is now abandoned in large parts of the world because of widespread drug-resistance in Plasmodium falciparum. In spite of its importance as a cost-effective and efficient drug, a coherent understanding of the cellular mechanisms affected by chloroquine and how they influence the fitness and survival of the parasite remains elusive. Here, we used a systems biology approach to integrate genome-scale transcriptomics to map out the effects of chloroquine, identify targeted metabolic pathways, and translate these findings into mechanistic insights. Specifically, we first developed a method that integrates transcriptomic and metabolomic data, which we independently validated against a recently published set of such data for Krebs-cycle mutants of P. falciparum. We then used the method to calculate the effect of chloroquine treatment on the metabolic flux profiles of P. falciparum during the intraerythrocytic developmental cycle. The model predicted dose-dependent inhibition of DNA replication, in agreement with earlier experimental results for both drug-sensitive and drug-resistant P. falciparum strains. Our simulations also corroborated experimental findings that suggest differences in chloroquine sensitivity between ring- and schizont-stage P. falciparum. Our analysis also suggests that metabolic fluxes that govern reduced thioredoxin and phosphoenolpyruvate synthesis are significantly decreased and are pivotal to chloroquine-based inhibition of P. falciparum DNA replication. The consequences of impaired phosphoenolpyruvate synthesis and redox metabolism are reduced carbon fixation and increased oxidative stress, respectively, both of which eventually facilitate killing of the parasite. Our analysis suggests that a combination of chloroquine (or an analogue) and another drug, which inhibits carbon fixation and/or increases oxidative stress, should increase the clearance of P. falciparum from the host system.
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8
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Rodrigues MJ, Windeisen V, Zhang Y, Guédez G, Weber S, Strohmeier M, Hanes JW, Royant A, Evans G, Sinning I, Ealick SE, Begley TP, Tews I. Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Nat Chem Biol 2017; 13:290-294. [PMID: 28092359 PMCID: PMC6078385 DOI: 10.1038/nchembio.2273] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/11/2016] [Indexed: 11/08/2022]
Abstract
Substrate channeling has emerged as a common mechanism for enzymatic intermediate transfer. A conspicuous gap in knowledge concerns the use of covalent lysine imines in the transfer of carbonyl-group-containing intermediates, despite their wideuse in enzymatic catalysis. Here we show how imine chemistry operates in the transfer of covalent intermediates in pyridoxal 5'-phosphate biosynthesis by the Arabidopsis thaliana enzyme Pdx1. An initial ribose 5-phosphate lysine imine is converted to the chromophoric I320 intermediate, simultaneously bound to two lysine residues and partially vacating the active site, which creates space for glyceraldehyde 3-phosphate to bind. Crystal structures show how substrate binding, catalysis and shuttling are coupled to conformational changes around strand β6 of the Pdx1 (βα)8-barrel. The dual-specificity active site and imine relay mechanism for migration of carbonyl intermediates provide elegant solutions to the challenge of coordinating a complex sequence of reactions that follow a path of over 20 Å between substrate- and product-binding sites.
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Affiliation(s)
- Matthew J Rodrigues
- Biological Sciences, University of Southampton, Southampton, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Volker Windeisen
- Biological Sciences, University of Southampton, Southampton, UK
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Gabriela Guédez
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Stefan Weber
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Marco Strohmeier
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Jeremiah W Hanes
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
- Pacific Biosciences, Menlo Park, California, USA
| | - Antoine Royant
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
- European Synchrotron Radiation Facility, Grenoble, France
| | - Gwyndaf Evans
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Steven E Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Ivo Tews
- Biological Sciences, University of Southampton, Southampton, UK
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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9
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Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis. Proc Natl Acad Sci U S A 2016; 113:E5821-E5829. [PMID: 27647886 DOI: 10.1073/pnas.1608125113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vitamin B6 is indispensible for all organisms, notably as the coenzyme form pyridoxal 5'-phosphate. Plants make the compound de novo using a relatively simple pathway comprising pyridoxine synthase (PDX1) and pyridoxine glutaminase (PDX2). PDX1 is remarkable given its multifaceted synthetic ability to carry out isomerization, imine formation, ammonia addition, aldol-type condensation, cyclization, and aromatization, all in the absence of coenzymes or recruitment of specialized domains. Two active sites (P1 and P2) facilitate the plethora of reactions, but it is not known how the two are coordinated and, moreover, if intermediates are tunneled between active sites. Here we present X-ray structures of PDX1.3 from Arabidopsis thaliana, the overall architecture of which is a dodecamer of (β/α)8 barrels, similar to the majority of its homologs. An apoenzyme structure revealed that features around the P1 active site in PDX1.3 have adopted inward conformations consistent with a catalytically primed state and delineated a substrate accessible cavity above this active site, not noted in other reported structures. Comparison with the structure of PDX1.3 with an intermediate along the catalytic trajectory demonstrated that a lysine residue swings from the distinct P2 site to the P1 site at this stage of catalysis and is held in place by a molecular catch and pin, positioning it for transfer of serviced substrate back to P2. The study shows that a simple lysine swinging arm coordinates use of chemically disparate sites, dispensing with the need for additional factors, and provides an elegant example of solving complex chemistry to generate an essential metabolite.
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10
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Smith AM, Brown WC, Harms E, Smith JL. Crystal structures capture three states in the catalytic cycle of a pyridoxal phosphate (PLP) synthase. J Biol Chem 2015; 290:5226-39. [PMID: 25568319 DOI: 10.1074/jbc.m114.626382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PLP synthase (PLPS) is a remarkable single-enzyme biosynthetic pathway that produces pyridoxal 5'-phosphate (PLP) from glutamine, ribose 5-phosphate, and glyceraldehyde 3-phosphate. The intact enzyme includes 12 synthase and 12 glutaminase subunits. PLP synthesis occurs in the synthase active site by a complicated mechanism involving at least two covalent intermediates at a catalytic lysine. The first intermediate forms with ribose 5-phosphate. The glutaminase subunit is a glutamine amidotransferase that hydrolyzes glutamine and channels ammonia to the synthase active site. Ammonia attack on the first covalent intermediate forms the second intermediate. Glyceraldehyde 3-phosphate reacts with the second intermediate to form PLP. To investigate the mechanism of the synthase subunit, crystal structures were obtained for three intermediate states of the Geobacillus stearothermophilus intact PLPS or its synthase subunit. The structures capture the synthase active site at three distinct steps in its complicated catalytic cycle, provide insights into the elusive mechanism, and illustrate the coordinated motions within the synthase subunit that separate the catalytic states. In the intact PLPS with a Michaelis-like intermediate in the glutaminase active site, the first covalent intermediate of the synthase is fully sequestered within the enzyme by the ordering of a generally disordered 20-residue C-terminal tail. Following addition of ammonia, the synthase active site opens and admits the Lys-149 side chain, which participates in formation of the second intermediate and PLP. Roles are identified for conserved Asp-24 in the formation of the first intermediate and for conserved Arg-147 in the conversion of the first to the second intermediate.
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Affiliation(s)
- Amber Marie Smith
- From the Department of Biological Chemistry, Life Sciences Institute
| | - William Clay Brown
- Life Sciences Institute, Center for Structural Biology, University of Michigan, Ann Arbor, Michigan 48109 and
| | - Etti Harms
- the Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Janet L Smith
- From the Department of Biological Chemistry, Life Sciences Institute, Center for Structural Biology, University of Michigan, Ann Arbor, Michigan 48109 and
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11
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Moccand C, Boycheva S, Surriabre P, Tambasco-Studart M, Raschke M, Kaufmann M, Fitzpatrick TB. The pseudoenzyme PDX1.2 boosts vitamin B6 biosynthesis under heat and oxidative stress in Arabidopsis. J Biol Chem 2014; 289:8203-16. [PMID: 24505140 DOI: 10.1074/jbc.m113.540526] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Vitamin B6 is an indispensable compound for survival, well known as a cofactor for numerous central metabolic enzymes and more recently for playing a role in several stress responses, particularly in association with oxidative stress. Regulatory aspects for the use of the vitamin in these roles are not known. Here we show that certain plants carry a pseudoenzyme (PDX1.2), which is involved in regulating vitamin B6 biosynthesis de novo under stress conditions. Specifically, we demonstrate that Arabidopsis PDX1.2 enhances the activity of its catalytic paralogs by forming a heterododecameric complex. PDX1.2 is strongly induced by heat as well as singlet oxygen stress, concomitant with an enhancement of vitamin B6 production. Analysis of pdx1.2 knockdown lines demonstrates that boosting vitamin B6 content is dependent on PDX1.2, revealing that this pseudoenzyme acts as a positive regulator of vitamin B6 biosynthesis during such stress conditions in plants.
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Affiliation(s)
- Cyril Moccand
- From the Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland and
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12
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Exploring inhibition of Pdx1, a component of the PLP synthase complex of the human malaria parasite Plasmodium falciparum. Biochem J 2013; 449:175-87. [PMID: 23039077 DOI: 10.1042/bj20120925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Malaria tropica is a devastating infectious disease caused by Plasmodium falciparum. This parasite synthesizes vitamin B6 de novo via the PLP (pyridoxal 5'-phosphate) synthase enzymatic complex consisting of PfPdx1 and PfPdx2 proteins. Biosynthesis of PLP is largely performed by PfPdx1, ammonia provided by PfPdx2 subunits is condensed together with R5P (D-ribose 5-phosphate) and G3P (DL-glyceraldehyde 3-phosphate). PfPdx1 accommodates both the R5P and G3P substrates and intricately co-ordinates the reaction mechanism, which is composed of a series of imine bond formations, leading to the production of PLP. We demonstrate that E4P (D-erythrose 4-phosphate) inhibits PfPdx1 in a dose-dependent manner. We propose that the acyclic phospho-sugar E4P, with a C1 aldehyde group similar to acyclic R5P, could interfere with R5P imine bond formations in the PfPdx1 reaction mechanism. Molecular docking and subsequent screening identified the E4P hydrazide analogue 4PEHz (4-phospho-D-erythronhydrazide), which selectively inhibited PfPdx1 with an IC50 of 43 μM. PfPdx1 contained in the heteromeric PLP synthase complex was shown to be more sensitive to 4PEHz and was inhibited with an IC50 of 16 μM. Moreover, the compound had an IC50 value of 10 μM against cultured P. falciparum intraerythrocytic parasites. To analyse further the selectivity of 4PEHz, transgenic cell lines overexpressing PfPdx1 and PfPdx2 showed that additional copies of the protein complex conferred protection against 4PEHz, indicating that the PLP synthase is directly affected by 4PEHz in vivo. These PfPdx1 inhibitors represent novel lead scaffolds which are capable of targeting PLP biosynthesis, and we propose this as a viable strategy for the development of new therapeutics against malaria.
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Guédez G, Hipp K, Windeisen V, Derrer B, Gengenbacher M, Böttcher B, Sinning I, Kappes B, Tews I. Assembly of the eukaryotic PLP-synthase complex from Plasmodium and activation of the Pdx1 enzyme. Structure 2012; 20:172-84. [PMID: 22244765 DOI: 10.1016/j.str.2011.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/04/2011] [Accepted: 11/05/2011] [Indexed: 11/26/2022]
Abstract
Biosynthesis of vitamins is fundamental to malaria parasites. Plasmodia synthesize the active form of vitamin B(6) (pyridoxal 5'-phosphate, PLP) using a PLP synthase complex. The EM analysis shown here reveals a random association pattern of up to 12 Pdx2 glutaminase subunits to the dodecameric Pdx1 core complex. Interestingly, Plasmodium falciparum PLP synthase organizes in fibers. The crystal structure shows differences in complex formation to bacterial orthologs as interface variations. Alternative positioning of an α helix distinguishes an open conformation from a closed state when the enzyme binds substrate. The pentose substrate is covalently attached through its C1 and forms a Schiff base with Lys84. Ammonia transfer between Pdx2 glutaminase and Pdx1 active sites is regulated by a transient tunnel. The mutagenesis analysis allows defining the requirement for conservation of critical methionines, whereas there is also plasticity in ammonia tunnel construction as seen from comparison across different species.
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Affiliation(s)
- Gabriela Guédez
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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14
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Mukherjee T, Hanes J, Tews I, Ealick SE, Begley TP. Pyridoxal phosphate: biosynthesis and catabolism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1585-96. [PMID: 21767669 DOI: 10.1016/j.bbapap.2011.06.018] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 06/26/2011] [Accepted: 06/29/2011] [Indexed: 11/19/2022]
Abstract
Vitamin B(6) is an essential cofactor that participates in a large number of biochemical reactions. Pyridoxal phosphate is biosynthesized de novo by two different pathways (the DXP dependent pathway and the R5P pathway) and can also be salvaged from the environment. It is one of the few cofactors whose catabolic pathway has been comprehensively characterized. It is also known to function as a singlet oxygen scavenger and has protective effects against oxidative stress in fungi. Enzymes utilizing vitamin B(6) are important targets for therapeutic agents. This review provides a concise overview of the mechanistic enzymology of vitamin B(6) biosynthesis and catabolism. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Tathagata Mukherjee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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15
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Moccand C, Kaufmann M, Fitzpatrick TB. It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase. PLoS One 2011; 6:e16042. [PMID: 21283685 PMCID: PMC3024981 DOI: 10.1371/journal.pone.0016042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/09/2010] [Indexed: 11/24/2022] Open
Abstract
The prevalent de novo biosynthetic pathway of vitamin B6 involves only two enzymes (Pdx1 and Pdx2) that form an ornate multisubunit complex functioning as a glutamine amidotransferase. The synthase subunit, Pdx1, utilizes ribose 5-phosphate and glyceraldehyde 3-phosphate, as well as ammonia derived from the glutaminase activity of Pdx2 to directly form the cofactor vitamer, pyridoxal 5′-phosphate. Given the fact that a single enzyme performs the majority of the chemistry behind this reaction, a complicated mechanism is anticipated. Recently, the individual steps along the reaction co-ordinate are beginning to be unraveled. In particular, the binding of the pentose substrate and the first steps of the reaction have been elucidated but it is not known if the latter part of the chemistry, involving the triose sugar, takes place in the same or a disparate site. Here, we demonstrate through the use of enzyme assays, enzyme kinetics, and mutagenesis studies that indeed a second site is involved in binding the triose sugar and moreover, is the location of the final vitamin product, pyridoxal 5′-phosphate. Furthermore, we show that product release is triggered by the presence of a PLP-dependent enzyme. Finally, we provide evidence that a single arginine residue of the C terminus of Pdx1 is responsible for coordinating co-operativity in this elaborate protein machinery.
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Affiliation(s)
- Cyril Moccand
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Markus Kaufmann
- Bio-Molecular Analysis Platform, University of Geneva, Geneva, Switzerland
| | - Teresa B. Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- * E-mail:
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16
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Fitzpatrick TB, Moccand C, Roux C. Vitamin B6 biosynthesis: charting the mechanistic landscape. Chembiochem 2010; 11:1185-93. [PMID: 20397182 DOI: 10.1002/cbic.201000084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Sciences III, 30 Quai Ernest Ansermet, 1211 Geneva 4, Switzerland.
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17
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Hanes JW, Keresztes I, Begley TP. 13C NMR snapshots of the complex reaction coordinate of pyridoxal phosphate synthase. Nat Chem Biol 2008; 4:425-30. [DOI: 10.1038/nchembio.93] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 05/08/2008] [Indexed: 11/09/2022]
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18
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Begley TP, Chatterjee A, Hanes JW, Hazra A, Ealick SE. Cofactor biosynthesis--still yielding fascinating new biological chemistry. Curr Opin Chem Biol 2008; 12:118-25. [PMID: 18314013 DOI: 10.1016/j.cbpa.2008.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 02/05/2008] [Accepted: 02/06/2008] [Indexed: 11/26/2022]
Abstract
This mini review covers recent advances in the mechanistic enzymology of cofactor biosynthesis.
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Affiliation(s)
- Tadhg P Begley
- Cornell University, Department of Chemistry and Chemical Biology, 120 Baker Lab, Ithaca, NY 14853, United States.
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