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The Multifaceted MEP Pathway: Towards New Therapeutic Perspectives. Molecules 2023; 28:molecules28031403. [PMID: 36771066 PMCID: PMC9919496 DOI: 10.3390/molecules28031403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Isoprenoids, a diverse class of natural products, are present in all living organisms. Their two universal building blocks are synthesized via two independent pathways: the mevalonate pathway and the 2-C-methyl-ᴅ-erythritol 4-phosphate (MEP) pathway. The presence of the latter in pathogenic bacteria and its absence in humans make all its enzymes suitable targets for the development of novel antibacterial drugs. (E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), the last intermediate of this pathway, is a natural ligand for the human Vγ9Vδ2 T cells and the most potent natural phosphoantigen known to date. Moreover, 5-hydroxypentane-2,3-dione, a metabolite produced by Escherichia coli 1-deoxy-ᴅ-xylulose 5-phosphate synthase (DXS), the first enzyme of the MEP pathway, structurally resembles (S)-4,5-dihydroxy-2,3-pentanedione, a signal molecule implied in bacterial cell communication. In this review, we shed light on the diversity of potential uses of the MEP pathway in antibacterial therapies, starting with an overview of the antibacterials developed for each of its enzymes. Then, we provide insight into HMBPP, its synthetic analogs, and their prodrugs. Finally, we discuss the potential contribution of the MEP pathway to quorum sensing mechanisms. The MEP pathway, providing simultaneously antibacterial drug targets and potent immunostimulants, coupled with its potential role in bacterial cell-cell communication, opens new therapeutic perspectives.
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2
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Pina AF, Sousa SF, Cerqueira NMFSA. The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study. Chembiochem 2021; 23:e202100555. [PMID: 34762772 DOI: 10.1002/cbic.202100555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/10/2021] [Indexed: 11/08/2022]
Abstract
The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens that rely on this mechanism to obtain PLP. For this reason, Pdx2 is considered a novel and promising drug target to treat these diseases. The results obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87 , (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature (19.1-19.5 kcal mol-1 ) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11 ), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile Cys87 to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) Glu198 does not have a direct role in the catalytic process. Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting Pdx2 and impair diseases like Malaria and Tuberculosis.
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Affiliation(s)
- André F Pina
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sérgio F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Nuno M F S A Cerqueira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
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3
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He M, Ma J, Chen Q, Zhang Q, Yu P. Engineered production of pyridoxal 5'-phosphate in Escherichia coli BL21. Prep Biochem Biotechnol 2021; 52:498-507. [PMID: 34431758 DOI: 10.1080/10826068.2021.1966801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) is the coenzyme of more than 140 enzymes and is widely used in various fields. In this study, to enhance the production of PLP in Escherichia coli BL21, the recombinant strain E. coli BL21/pETDuet-1-pdxj-zwf-dxs was constructed. The concentration of PLP in this strain was 82.69 mg/L, which was increased by 1.38-fold as compared to that in E. coli BL21. Glucose, yeast extract, and pH had an obvious impact on the concentration of PLP, and their optimal levels were 34.89 g/L, 31.17 g/L, and 10.07, respectively. The concentration of PLP under the optimal condition reached 2.23 g/L. The time-course analysis showed that the highest concentration of PLP was 2.32 g/L in recombinant strain after the induction for 12 h by 0.1 mM IPTG in a 1 L shake flask, which was increased by 38.76-fold as compared to that in E. coli BL21. This study provides a good basis for the efficient production of PLP in E. coli BL21.
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Affiliation(s)
- Min He
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Jian Ma
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Qingwei Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Qili Zhang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
| | - Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, People's Republic of China
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Zuo MT, Wu Y, Wang ZY, Wang N, Huang SJ, Yu H, Zhao XJ, Huang CY, Liu ZY. A comprehensive toxicity evaluation in rats after long-term oral Gelsemium elegans exposure. Biomed Pharmacother 2021; 137:111284. [PMID: 33561641 DOI: 10.1016/j.biopha.2021.111284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Gelsemium elegans (G. elegans) is a flowering plant of the Loganiaceae family, which had been used in traditional Chinese herb medicine for many years for the treatment of rheumatoid pain, neuropathic pain, spasticity, skin ulcers, anxiety and cancer. Acute toxicity of the plant severely limits the application and development of G. elegans; however, long-term toxicity of exposure to G. elegans has not been illuminated. PURPOSE This study is a comprehensive observation of the effects of long-term exposure (21 days at 70 mg/kg) to G. elegans in rats. METHODS AND RESULTS The histopathological examination showed only a mild glial cell proliferation in the brain, and no lesions were observed in other organs. No abnormal changes in the biochemical parameters were observed that would have significant effects. The identification and analysis of absorbed natural ingredients showed that the active ingredients of the G. elegans could distribute to various tissues, and six compounds were identified in the brain, suggesting that they could cross the blood-brain barrier. Based on the intestinal content metabolomics, the tryptophan (Trp) biosynthesis, bile acid synthesis and bile secretion pathways have attracted our attention. Plasma metabolomic results showed that uric acid (UA) was significantly increased. The results of the brain metabolomic tests showed that the level of pyridoxal (PL) was decreased; considering the expression levels of the related enzymes, it was hypothesized that the level of pyridoxal 5'-phosphate (PLP) was decreased. PLP was important for the regulation of the neuronal γ-aminobutyric acid (GABA)/glutamate (Glu) interconversion and therefore neuronal excitability. The data of the study suggested that toxic reaction caused by G. elegans was due to a disruption of the balance of the neurotransmitter GABA/Glu transformation. CONCLUSIONS Overall, G. elegans did not cause significant toxic reaction in the rats after long-term exposure. The results were significant for the future clinical applications of G. elegans and suggested that G. elegans could be potentially developed as a drug. The study provided a scientific basis for investigation of the mechanisms of toxicity and detoxification.
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Affiliation(s)
- Meng-Ting Zuo
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yong Wu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Zi-Yuan Wang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Na Wang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Si-Juan Huang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Hui Yu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Xue-Jiao Zhao
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Chong-Yin Huang
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Zhao-Ying Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China; Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, Hunan, China.
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5
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Abstract
Vitamin B6 is an ensemble of six interconvertible vitamers: pyridoxine (PN), pyridoxamine (PM), pyridoxal (PL), and their 5'-phosphate derivatives, PNP, PMP, and PLP. Pyridoxal 5'-phosphate is a coenzyme in a variety of enzyme reactions concerning transformations of amino and amino acid compounds. This review summarizes all known and putative PLP-binding proteins found in the Escherichia coli MG1655 proteome. PLP can have toxic effects since it contains a very reactive aldehyde group at its 4' position that easily forms aldimines with primary and secondary amines and reacts with thiols. Most PLP is bound either to the enzymes that use it as a cofactor or to PLP carrier proteins, protected from the cellular environment but at the same time readily transferable to PLP-dependent apoenzymes. E. coli and its relatives synthesize PLP through the seven-step deoxyxylulose-5-phosphate (DXP)-dependent pathway. Other bacteria synthesize PLP in a single step, through a so-called DXP-independent pathway. Although the DXP-dependent pathway was the first to be revealed, the discovery of the widespread DXP-independent pathway determined a decline of interest in E. coli vitamin B6 metabolism. In E. coli, as in most organisms, PLP can also be obtained from PL, PN, and PM, imported from the environment or recycled from protein turnover, via a salvage pathway. Our review deals with all aspects of vitamin B6 metabolism in E. coli, from transcriptional to posttranslational regulation. A critical interpretation of results is presented, in particular, concerning the most obscure aspects of PLP homeostasis and delivery to PLP-dependent enzymes.
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Jun YW, Hebenbrock M, Kool ET. A fluorescent hydrazone exchange probe of pyridoxal phosphate for the assessment of vitamin B6 status. Chem Commun (Camb) 2019; 56:317-320. [PMID: 31808778 PMCID: PMC7061904 DOI: 10.1039/c9cc08458d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abnormal vitamin B6 status, marked by deficient intracellular concentrations of pyridoxal phosphate (PLP), is classified as a direct biomarker based on its biomedical significance. However, there exist no direct methods for measuring vitamin B6 status in intact cells. Here we describe the development of a fluorogenic probe, RAB6, which shows remarkable selectivity for PLP among the B6 vitamers and other cellular aldehydes.
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Affiliation(s)
- Yong Woong Jun
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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Richts B, Rosenberg J, Commichau FM. A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis. Front Mol Biosci 2019; 6:32. [PMID: 31134210 PMCID: PMC6522883 DOI: 10.3389/fmolb.2019.00032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD+ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
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8
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Kumar V, Sharma M, Rakesh BR, Malik CK, Neelagiri S, Neerupudi KB, Garg P, Singh S. Pyridoxal kinase: A vitamin B6 salvage pathway enzyme from Leishmania donovani. Int J Biol Macromol 2018; 119:320-334. [DOI: 10.1016/j.ijbiomac.2018.07.095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/21/2022]
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9
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Rosenberg J, Ischebeck T, Commichau FM. Vitamin B6 metabolism in microbes and approaches for fermentative production. Biotechnol Adv 2016; 35:31-40. [PMID: 27890703 DOI: 10.1016/j.biotechadv.2016.11.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/21/2016] [Accepted: 11/21/2016] [Indexed: 12/20/2022]
Abstract
Vitamin B6 is a designation for the six vitamers pyridoxal, pyridoxine, pyridoxamine, pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate, and pyridoxamine. PLP, being the most important B6 vitamer, serves as a cofactor for many proteins and enzymes. In contrast to other organisms, animals and humans have to ingest vitamin B6 with their food. Several disorders are associated with vitamin B6 deficiency. Moreover, pharmaceuticals interfere with metabolism of the cofactor, which also results in vitamin B6 deficiency. Therefore, vitamin B6 is a valuable compound for the pharmaceutical and the food industry. Although vitamin B6 is currently chemically synthesized, there is considerable interest on the industrial side to shift from chemical processes to sustainable fermentation technologies. Here, we review recent findings regarding biosynthesis and homeostasis of vitamin B6 and describe the approaches that have been made in the past to develop microbial production processes. Moreover, we will describe novel routes for vitamin B6 biosynthesis and discuss their potential for engineering bacteria that overproduce the commercially valuable substance. We also highlight bottlenecks of the vitamin B6 biosynthetic pathways and propose strategies to circumvent these limitations.
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Affiliation(s)
- Jonathan Rosenberg
- Department of General Microbiology, Georg-August-University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Georg-August-University of Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Prunetti L, El Yacoubi B, Schiavon CR, Kirkpatrick E, Huang L, Bailly M, El Badawi-Sidhu M, Harrison K, Gregory JF, Fiehn O, Hanson AD, de Crécy-Lagard V. Evidence that COG0325 proteins are involved in PLP homeostasis. MICROBIOLOGY-SGM 2016; 162:694-706. [PMID: 26872910 DOI: 10.1099/mic.0.000255] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Pyridoxal 5'-phosphate (PLP) is an essential cofactor for nearly 60 Escherichia coli enzymes but is a highly reactive molecule that is toxic in its free form. How PLP levels are regulated and how PLP is delivered to target enzymes are still open questions. The COG0325 protein family belongs to the fold-type III class of PLP enzymes and binds PLP but has no known biochemical activity although it occurs in all kingdoms of life. Various pleiotropic phenotypes of the E. coli COG0325 (yggS) mutant have been reported, some of which were reproduced and extended in this study. Comparative genomic, genetic and metabolic analyses suggest that these phenotypes reflect an imbalance in PLP homeostasis. The E. coli yggS mutant accumulates the PLP precursor pyridoxine 5'-phosphate (PNP) and is sensitive to an excess of pyridoxine but not of pyridoxal. The pyridoxine toxicity phenotype is complemented by the expression of eukaryotic yggS orthologs. It is also suppressed by the presence of amino acids, specifically isoleucine, threonine and leucine, suggesting the PLP-dependent enzyme transaminase B (IlvE) is affected. These genetic results lay a foundation for future biochemical studies of the role of COG0325 proteins in PLP homeostasis.
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Affiliation(s)
- Laurence Prunetti
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Cara R Schiavon
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Ericka Kirkpatrick
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Lili Huang
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, USA
| | - Marc Bailly
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Mona El Badawi-Sidhu
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, CA, USA
| | - Katherine Harrison
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jesse F Gregory
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, USA
| | - Oliver Fiehn
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, CA, USA
| | - Andrew D Hanson
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetics Institute, University of Florida, Gainesville, FL, USA
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Jones DC, Alphey MS, Wyllie S, Fairlamb AH. Chemical, genetic and structural assessment of pyridoxal kinase as a drug target in the African trypanosome. Mol Microbiol 2012; 86:51-64. [PMID: 22857512 PMCID: PMC3470933 DOI: 10.1111/j.1365-2958.2012.08189.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2012] [Indexed: 01/18/2023]
Abstract
Pyridoxal-5'-phosphate (vitamin B(6) ) is an essential cofactor for many important enzymatic reactions such as transamination and decarboxylation. African trypanosomes are unable to synthesise vitamin B(6) de novo and rely on uptake of B(6) vitamers such as pyridoxal and pyridoxamine from their hosts, which are subsequently phosphorylated by pyridoxal kinase (PdxK). A conditional null mutant of PdxK was generated in Trypanosoma brucei bloodstream forms showing that this enzyme is essential for growth of the parasite in vitro and for infectivity in mice. Activity of recombinant T. brucei PdxK was comparable to previously published work having a specific activity of 327 ± 13 mU mg(-1) and a K(m)(app) with respect to pyridoxal of 29.6 ± 3.9 µM. A coupled assay was developed demonstrating that the enzyme has equivalent catalytic efficiency with pyridoxal, pyridoxamine and pyridoxine, and that ginkgotoxin is an effective pseudo substrate. A high resolution structure of PdxK in complex with ATP revealed important structural differences with the human enzyme. These findings suggest that pyridoxal kinase is an essential and druggable target that could lead to much needed alternative treatments for this devastating disease.
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Affiliation(s)
- Deuan C Jones
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of DundeeDundee, UK
| | | | - Susan Wyllie
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of DundeeDundee, UK
| | - Alan H Fairlamb
- Division of Biological Chemistry & Drug Discovery, College of Life Sciences, University of DundeeDundee, UK
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12
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Ghatge MS, Contestabile R, di Salvo ML, Desai JV, Gandhi AK, Camara CM, Florio R, González IN, Parroni A, Schirch V, Safo MK. Pyridoxal 5'-phosphate is a slow tight binding inhibitor of E. coli pyridoxal kinase. PLoS One 2012; 7:e41680. [PMID: 22848564 PMCID: PMC3404986 DOI: 10.1371/journal.pone.0041680] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 06/24/2012] [Indexed: 11/18/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP) is a cofactor for dozens of B6 requiring enzymes. PLP reacts with apo-B6 enzymes by forming an aldimine linkage with the ε-amino group of an active site lysine residue, thus yielding the catalytically active holo-B6 enzyme. During protein turnover, the PLP is salvaged by first converting it to pyridoxal by a phosphatase and then back to PLP by pyridoxal kinase. Nonetheless, PLP poses a potential toxicity problem for the cell since its reactive 4′-aldehyde moiety forms covalent adducts with other compounds and non-B6 proteins containing thiol or amino groups. The regulation of PLP homeostasis in the cell is thus an important, yet unresolved issue. In this report, using site-directed mutagenesis, kinetic, spectroscopic and chromatographic studies we show that pyridoxal kinase from E. coli forms a complex with the product PLP to form an inactive enzyme complex. Evidence is presented that, in the inhibited complex, PLP has formed an aldimine bond with an active site lysine residue during catalytic turnover. The rate of dissociation of PLP from the complex is very slow, being only partially released after a 2-hour incubation with PLP phosphatase. Interestingly, the inactive pyridoxal kinase•PLP complex can be partially reactivated by transferring the tightly bound PLP to an apo-B6 enzyme. These results open new perspectives on the mechanism of regulation and role of pyridoxal kinase in the Escherichia coli cell.
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Affiliation(s)
- Mohini S. Ghatge
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Roberto Contestabile
- Istituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Roma, Italy
| | - Martino L. di Salvo
- Istituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Roma, Italy
| | - Jigar V. Desai
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Amit K. Gandhi
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Christina M. Camara
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Rita Florio
- Istituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Roma, Italy
| | - Isabel N. González
- Consiglio Nazionale delle Ricerche, Istituto di Biologia Agroambientale e Forestale, Monterotondo Scalo, Roma, Italy
- Institute of Biocomputation and Physics of Complex Systems, Universidad de Zaragoza, Zaragoza, Spain
| | - Alessia Parroni
- Istituto Pasteur-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, Roma, Italy
| | - Verne Schirch
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Martin K. Safo
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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13
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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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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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16
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Wu F, Christen P, Gehring H. A novel approach to inhibit intracellular vitamin B6‐dependent enzymes: proof of principle with human and plasmodium ornithine decarboxylase and human histidine decarboxylase. FASEB J 2011; 25:2109-22. [DOI: 10.1096/fj.10-174383] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fang Wu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghaiChina
| | | | - Heinz Gehring
- Department of BiochemistryUniversity of ZurichZurichSwitzerland
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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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