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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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Ghatge MS, Al Mughram M, Omar AM, Safo MK. Inborn errors in the vitamin B6 salvage enzymes associated with neonatal epileptic encephalopathy and other pathologies. Biochimie 2021; 183:18-29. [PMID: 33421502 DOI: 10.1016/j.biochi.2020.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/28/2022]
Abstract
Pyridoxal 5'-phosphate (PLP), the active cofactor form of vitamin B6 is required by over 160 PLP-dependent (vitamin B6) enzymes serving diverse biological roles, such as carbohydrates, amino acids, hemes, and neurotransmitters metabolism. Three key enzymes, pyridoxal kinase (PL kinase), pyridoxine 5'-phosphate oxidase (PNPO), and phosphatases metabolize and supply PLP to PLP-dependent enzymes through the salvage pathway. In born errors in the salvage enzymes are known to cause inadequate levels of PLP in the cell, particularly in neuronal cells. The resulting PLP deficiency is known to cause or implicated in several pathologies, most notably seizures. One such disorder, PNPO-dependent neonatal epileptic encephalopathy (NEE) results from natural mutations in PNPO and leads to null or reduced enzymatic activity. NEE does not respond to conventional antiepileptic drugs but may respond to treatment with the B6 vitamers PLP and/or pyridoxine (PN). In born errors that lead to PLP deficiency in cells have also been reported in PL kinase, however, to date none has been associated with epilepsy or seizure. One such pathology is polyneuropathy that responds to PLP therapy. Phosphatase deficiency or hypophosphatasia disorder due to pathogenic mutations in alkaline phosphatase is known to cause seizures that respond to PN therapy. In this article, we review the biochemical features of in born errors pertaining to the salvage enzyme's deficiency that leads to NEE and other pathologies. We also present perspective on vitamin B6 treatment for these disorders, along with attempts to develop zebrafish model to study the NEE syndrome in vivo.
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Affiliation(s)
- Mohini S Ghatge
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Mohammed Al Mughram
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Abdelsattar M Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah, 21589, Saudi Arabia; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo, 11884, Egypt
| | - Martin K Safo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, 23298, USA; Institute for Structural Biology, Drug Discovery, and Development, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, 23298, USA.
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3
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Barile A, Tramonti A, di Salvo ML, Nogués I, Nardella C, Malatesta F, Contestabile R. Allosteric feedback inhibition of pyridoxine 5'-phosphate oxidase from Escherichia coli. J Biol Chem 2019; 294:15593-15603. [PMID: 31484724 DOI: 10.1074/jbc.ra119.009697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/02/2019] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, the synthesis of pyridoxal 5'-phosphate (PLP), the catalytically active form of vitamin B6, takes place through the so-called deoxyxylulose 5-phosphate-dependent pathway, whose last step is pyridoxine 5'-phosphate (PNP) oxidation to PLP, catalyzed by the FMN-dependent enzyme PNP oxidase (PNPOx). This enzyme plays a pivotal role in controlling intracellular homeostasis and bioavailability of PLP. PNPOx has been proposed to undergo product inhibition resulting from PLP binding at the active site. PLP has also been reported to bind tightly at a secondary site, apparently without causing PNPOx inhibition. The possible location of this secondary site has been indicated by crystallographic studies as two symmetric surface pockets present on the PNPOx homodimer, but this site has never been verified by other experimental means. Here, we demonstrate, through kinetic measurements, that PLP inhibition is actually of a mixed-type nature and results from binding of this vitamer at an allosteric site. This interpretation was confirmed by the characterization of a mutated PNPOx form, in which substrate binding at the active site is heavily hampered but PLP binding is preserved. Structural and functional connections between the active site and the allosteric site were indicated by equilibrium binding experiments, which revealed different PLP-binding stoichiometries with WT and mutant PNPOx forms. These observations open up new horizons on the mechanisms that regulate E. coli PNPOx, which may have commonalities with the mechanisms regulating human PNPOx, whose crucial role in vitamin B6 metabolism and epilepsy is well-known.
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Affiliation(s)
- Anna Barile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Angela Tramonti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy.,Istituto di Biologia e Patologia Molecolari, CNR, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Martino Luigi di Salvo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Isabel Nogués
- Istituto di Ricerca sugli Ecosistemi Terrestri, CNR, Via G. Marconi 2, 05010 Porano (TR), Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesco Malatesta
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
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4
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Parra M, Stahl S, Hellmann H. Vitamin B₆ and Its Role in Cell Metabolism and Physiology. Cells 2018; 7:cells7070084. [PMID: 30037155 PMCID: PMC6071262 DOI: 10.3390/cells7070084] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/11/2022] Open
Abstract
Vitamin B6 is one of the most central molecules in cells of living organisms. It is a critical co-factor for a diverse range of biochemical reactions that regulate basic cellular metabolism, which impact overall physiology. In the last several years, major progress has been accomplished on various aspects of vitamin B6 biology. Consequently, this review goes beyond the classical role of vitamin B6 as a cofactor to highlight new structural and regulatory information that further defines how the vitamin is synthesized and controlled in the cell. We also discuss broader applications of the vitamin related to human health, pathogen resistance, and abiotic stress tolerance. Overall, the information assembled shall provide helpful insight on top of what is currently known about the vitamin, along with addressing currently open questions in the field to highlight possible approaches vitamin B6 research may take in the future.
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Affiliation(s)
- Marcelina Parra
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
| | - Seth Stahl
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
| | - Hanjo Hellmann
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
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Huang S, Liu Z, Ma Z, Zhang J, Huang L. Isolation and characterization of the 5'-flanking region of the human PDXK gene. Gene 2017; 628:218-223. [PMID: 28716709 DOI: 10.1016/j.gene.2017.07.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/17/2022]
Abstract
Pyridoxal kinase is a key enzyme for the biosynthesis of pyridoxal 5'-phosphate. Pyridoxal 5'-phosphate is the catalytically active form of vitamin B6, and acts as a cofactor in >140 different enzyme reactions. It is still unknown how the kinase synthesis is regulated in the cells, and nothing has been reported about the gene promoter. In the present study, based on the bioinformatics analysis of the 5'-flanking region of the human PDXK gene, we cloned the promoter region by PCR. Through the construction of a series of luciferase expression vectors containing the human PDXK promoter region, we characterized the promoter in terms of its structure and function. The transcription start site is at 198bp upstream of the ATG translation initiation site. An important regulatory region is located at -665/-433bp upstream of the transcription start site. The promoter lacks the canonical TATA box, but contains three GC-boxes and one E-box. A deletion and mutation experiment revealed that the transcription factor Sp1 binding site C (-553/-543) is critical in maintaining the robust promoter activity. Knockdown of Sp1 by RNA interference and chromatin immunoprecipitation analysis further proved that the Sp1 is involved in the regulation of the PDXK gene expression.
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Affiliation(s)
- ShuoHao Huang
- School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, People's Republic of China; Centre for Commercialization of Regenerative Medicine, 661 University Avenue, Toronto, Canada
| | - ZhengQing Liu
- School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - ZhenQiao Ma
- School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - JianYun Zhang
- School of Foreign Languages, Anhui Agricultural University, Hefei 230036, People's Republic of China.
| | - LongQuan Huang
- School of Tea and Food Science & Technology, Anhui Agricultural University, Hefei 230036, People's Republic of China.
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6
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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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Huang S, Yang H, Yao L, Zhang J, Huang L. Effect of exogenous hormones on transcription levels of pyridoxal 5'-phosphate biosynthetic enzymes in the silkworm (Bombyx mori). Comp Biochem Physiol B Biochem Mol Biol 2016; 194-195:20-4. [PMID: 26780217 DOI: 10.1016/j.cbpb.2016.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/17/2015] [Accepted: 01/06/2016] [Indexed: 11/25/2022]
Abstract
Vitamin B6 includes 6 pyridine derivatives, among which pyridoxal 5'-phosphate is a coenzyme for over 140 enzymes. Animals acquire their vitamin B6 from food. Through a salvage pathway, pyridoxal 5'-phosphate is synthesized from pyridoxal, pyridoxine or pyridoxamine, in a series of reactions catalyzed by pyridoxal kinase and pyridoxine 5'-phosphate oxidase. The regulation of pyridoxal 5'-phospahte biosynthesis and pyridoxal 5'-phospahte homeostasis are at the center of study for vitamin B6 nutrition. How pyridoxal 5'-phosphate biosynthesis is regulated by hormones has not been reported so far. Our previous studies have shown that pyridoxal 5'-phosphate level in silkworm larva displays cyclic developmental changes. In the current study, effects of exogenous juvenile hormone and molting hormone on the transcription level of genes coding for the enzymes involved in the biosynthesis of pyridoxal 5'-phospahte were examined. Results show that pyridoxal kinase and pyridoxine 5'-phosphate oxidase are regulated at the transcription level by development and are responsive to hormones. Molting hormone stimulates the expression of genes coding for pyridoxal kinase and pyridoxine 5'-phosphate oxidase, and juvenile hormone appears to work against molting hormone. Whether pyridoxal 5'-phosphate biosynthesis is regulated by hormones in general is an important issue for further studies.
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Affiliation(s)
- ShuoHao Huang
- School of Tea and Food Science, Anhui Agricultural University, Hefei 230036, People's Republic of China; Center for Cell and Gene Therapy, Takara Bio Inc., Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - HuanHuan Yang
- School of Tea and Food Science, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - LiLi Yao
- School of Tea and Food Science, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - JianYun Zhang
- School of Foreign Languages, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - LongQuan Huang
- School of Tea and Food Science, Anhui Agricultural University, Hefei 230036, People's Republic of China.
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8
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di Salvo ML, Nogués I, Parroni A, Tramonti A, Milano T, Pascarella S, Contestabile R. On the mechanism of Escherichia coli pyridoxal kinase inhibition by pyridoxal and pyridoxal 5'-phosphate. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1160-6. [PMID: 25655354 DOI: 10.1016/j.bbapap.2015.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 10/24/2022]
Abstract
Pyridoxal 5'-phosphate (PLP), the catalytically active form of vitamin B6, plays a crucial role in several cellular processes. In most organisms, PLP is recycled from nutrients and degraded B6-enzymes in a salvage pathway that involves pyridoxal kinase (PLK), pyridoxine phosphate oxidase and phosphatase activities. Regulation of the salvage pathway is poorly understood. Escherichia coli possesses two distinct pyridoxal kinases, PLK1, which is the focus of the present work, and PLK2. From previous studies dating back to thirty years ago, pyridoxal (PL) was shown to inhibit E. coli PLK1 forming a covalent link with the enzyme. This inhibition was proposed to play a regulative role in vitamin B6 metabolism, although its details had never been clarified. Recently, we have shown that also PLP produced during PLK1 catalytic cycle acts as an inhibitor, forming a Schiff base with Lys229, without being released in the solvent. The question arises as to which is the actual inhibition mechanism by PL and PLP. In the present work, we demonstrated that also PL binds to Lys229 as a Schiff base. However, the isolated covalent PLK1-PL complex is not inactive but, in the presence of ATP, is able to catalyse the single turnover production of PLP, which binds tightly to the enzyme and is ultimately responsible for its inactivation. The inactivation mechanism mediated by Lys229 may play a physiological role in controlling cellular levels of PLP. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Martino Luigi di Salvo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Isabel Nogués
- Istituto di Biologia Ambientale e Forestale, Consiglio Nazionale delle Ricerche, Via Salaria Km 29.300, 00015 Monterotondo Scalo, Roma, Italy
| | - Alessia Parroni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro 5, 00185 Roma, Italy; Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy.
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9
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Castro-Fernandez V, Bravo-Moraga F, Ramirez-Sarmiento CA, Guixe V. Emergence of pyridoxal phosphorylation through a promiscuous ancestor during the evolution of hydroxymethyl pyrimidine kinases. FEBS Lett 2014; 588:3068-73. [PMID: 24952356 DOI: 10.1016/j.febslet.2014.06.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 11/24/2022]
Abstract
In the family of ATP-dependent vitamin kinases, several bifunctional enzymes that phosphorylate hydroxymethyl pyrimidine (HMP) and pyridoxal (PL) have been described besides enzymes specific towards HMP. To determine how bifunctionality emerged, we reconstructed the sequence of three ancestors of HMP kinases, experimentally resurrected, and assayed the enzymatic activity of their last common ancestor. The latter has ∼ 8-fold higher specificity for HMP due to a glutamine residue (Gln44) that is a key determinant of the specificity towards HMP, although it is capable of phosphorylating both substrates. These results show how a specific enzyme with catalytic promiscuity gave rise to current bifunctional enzymes.
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Affiliation(s)
| | - Felipe Bravo-Moraga
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Victoria Guixe
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
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10
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Elsinghorst PW, di Salvo ML, Parroni A, Contestabile R. Inhibition of human pyridoxal kinase by 2-acetyl-4-((1R,2S,3R)-1,2,3,4-tetrahydroxybutyl)imidazole (THI). J Enzyme Inhib Med Chem 2014; 30:336-40. [PMID: 24899377 DOI: 10.3109/14756366.2014.915396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
2-Acetyl-4-((1R,2S,3R)-1,2,3,4-tetrahydroxybutyl)imidazole (THI) is observed as a minor contaminant in caramel food colourings (E 150c). Feeding experiments with rodents have revealed a significant lymphopenic effect that has been linked to the presence of THI in these food colourings. Pyridoxal kinase inhibition by THI has been suggested, but not demonstrated, as a mode of action as it leads to lowered levels of pyridoxal-5'-phosphate, which are known to cause lymphopenia. Recently, THI was also shown to inhibit sphingosine-1-phosphate lyase causing comparable immunosuppressive effects and derivatives of THI are being developed for the treatment of rheumatoid arthritis in humans. Interestingly, sphingosine-1-phosphate lyase activity depends on pyridoxal-5'-phosphate, which in turn is provided by pyridoxal kinase. This report shows that THI does inhibit pyridoxal kinase with competitive and mixed-type non-competitive behaviour towards its two substrates, pyridoxal and ATP, respectively. The corresponding inhibition constants are in the low millimolar range.
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Affiliation(s)
- Paul W Elsinghorst
- Pharmaceutical Chemistry I, Pharmaceutical Institute , University of Bonn, Bonn , Germany and
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11
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Achmon Y, Ben-Barak Zelas Z, Fishman A. Cloning Rosa hybrid phenylacetaldehyde synthase for the production of 2-phenylethanol in a whole cell Escherichia coli system. Appl Microbiol Biotechnol 2013; 98:3603-11. [DOI: 10.1007/s00253-013-5269-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/12/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
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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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di Salvo ML, Contestabile R, Safo MK. Vitamin B6 salvage enzymes: Mechanism, structure and regulation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1597-608. [DOI: 10.1016/j.bbapap.2010.12.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
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Cox BM, Bilsborrow JB, Walker KD. Enhanced Conversion of Racemic α-Arylalanines to (R)-β-Arylalanines by Coupled Racemase/Aminomutase Catalysis. J Org Chem 2009; 74:6953-9. [DOI: 10.1021/jo9009563] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brad M. Cox
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
- Michigan State University, East Lansing, Michigan 48824
| | - Joshua B. Bilsborrow
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
- Michigan State University, East Lansing, Michigan 48824
| | - Kevin D. Walker
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
- Michigan State University, East Lansing, Michigan 48824
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Opinion on Pyridoxal 5’‐phosphate as a source for vitamin B6 added for nutritional purposes in food supplements ‐ Scientific Panel on Food Additives, Flavourings, Processing Aids and Materials in Contact with Food. EFSA J 2008; 6:760. [DOI: 10.2903/j.efsa.2008.760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Malerba F, Bellelli A, Giorgi A, Bossa F, Contestabile R. The mechanism of addition of pyridoxal 5'-phosphate to Escherichia coli apo-serine hydroxymethyltransferase. Biochem J 2007; 404:477-85. [PMID: 17341210 PMCID: PMC1896279 DOI: 10.1042/bj20061681] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Previous studies suggest that the addition of pyridoxal 5'-phosphate to apo-serine hydroxymethyltransferase from Escherichia coli is the last event in the enzyme's folding process. We propose a mechanism for this reaction based on quenched-flow, stopped-flow and rapid-scanning stopped-flow experiments. All experiments were performed with an excess of apo-enzyme over cofactor, since excess pyridoxal 5'-phosphate results in a second molecule of cofactor binding to Lys346, which is part of the tetrahydropteroylglutamate-binding site. The equilibrium between the aldehyde and hydrate forms of the cofactor affects the kinetics of addition to the active site. Direct evidence of the formation of an intermediate aldimine between the cofactor and the active-site lysine was obtained. The results have been interpreted according to a three-step mechanism in which: (i) both aldehyde and hydrate forms of the cofactor bind rapidly and non-covalently to the apo-enzyme; (ii) only the aldehyde form reacts with the active-site lysine to give an intermediate internal aldimine with unusual spectral properties; and (iii) a final conformational change gives the native holo-enzyme.
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Affiliation(s)
- Francesca Malerba
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Bellelli
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Bossa
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Università degli Studi di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy
- To whom correspondence should be addressed (email )
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Hwang IK, Yoo KY, Kim DH, Lee BH, Kwon YG, Won MH. Time course of changes in pyridoxal 5'-phosphate (vitamin B6 active form) and its neuroprotection in experimental ischemic damage. Exp Neurol 2007; 206:114-25. [PMID: 17531224 DOI: 10.1016/j.expneurol.2007.04.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Revised: 03/19/2007] [Accepted: 04/14/2007] [Indexed: 10/23/2022]
Abstract
In the present study, we investigated ischemia-induced changes of pyridoxal 5'-phosphate synthesizing enzyme and degrading enzyme and neuroprotective effects and roles of pyridoxal 5'-phosphate against ischemic damage in the gerbil hippocampal CA1 region. Pyridoxal 5'-phosphate oxidase and pyridoxal phosphate phosphatase immunoreactivities were changed in neurons up to 2 days after ischemia, while 4 days after ischemia their immunoreactivities were expressed in astrocytes. Pyridoxal 5'-phosphate oxidase immunoreactivity and its protein level were highest 12 h after ischemia, while those in pyridoxal phosphate phosphatase were highest 2 days after ischemia. Total activities of these enzymes were changed after ischemia, but specific activities of the enzymes were not altered. Treatment with pyridoxal 5'-phosphate into brains (4 microg/5 microl, i.c.v.) at 30 min before transient ischemia protected about 80% of CA1 pyramidal cells 4 days after ischemia and induced elevation of glutamic acid decarboxylase 67 immunoreactivity in the CA1 region. However, pyridoxal 5'-phosphate treatment into ischemic brains decreased GABA transaminase immunoreactivity in the CA1 region after ischemia. These results indicate that pyridoxal 5'-phosphate may be associated with the inhibitory discharge of GABA in the hippocampal CA1 neurons, and the increased level of GABA may protect hippocampal CA1 pyramidal cells from ischemic damage.
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Affiliation(s)
- In Koo Hwang
- Department of Anatomy and Neurobiology, College of Medicine, Hallym University, Chuncheon 200-702, South Korea
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di Salvo ML, Hunt S, Schirch V. Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases. Protein Expr Purif 2005; 36:300-6. [PMID: 15249053 DOI: 10.1016/j.pep.2004.04.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Revised: 04/22/2004] [Indexed: 11/20/2022]
Abstract
Pyridoxal kinase is an ATP dependent enzyme that phosphorylates pyridoxal, pyridoxine, and pyridoxamine forming their respective 5'-phosphorylated esters. The kinase is a part of the salvage pathway for re-utilizing pyridoxal 5'-phosphate, which serves as a coenzyme for dozens of enzymes involved in amino acid and sugar metabolism. Clones of two pyridoxal kinases from Escherichia coli and one from human were inserted into a pET 22b plasmid and expressed in E. coli. All three enzymes were purified to near homogeneity and kinetic constants were determined for the three vitamin substrates. Previous studies had suggested that ZnATP was the preferred trinucleotide substrate, but our studies show that under physiological conditions MgATP is the preferred substrate. One of the two E. coli kinases has very low activity for pyridoxal, pyridoxine, and pyridoxamine. We conclude that in vivo this kinase may have an alternate substrate involved in another metabolic pathway and that pyridoxal has only a poor secondary activity for this kinase.
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Affiliation(s)
- Martino L di Salvo
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università degli Studi di Roma, La Sapienza, Rome, Italy
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Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V. Crystal structure of the PdxY Protein from Escherichia coli. J Bacteriol 2004; 186:8074-82. [PMID: 15547280 PMCID: PMC529075 DOI: 10.1128/jb.186.23.8074-8082.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.
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Affiliation(s)
- Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA .
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Musayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK. Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. Protein Sci 2003; 12:1455-63. [PMID: 12824491 PMCID: PMC2323923 DOI: 10.1110/ps.0356203] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2003] [Revised: 04/04/2003] [Accepted: 04/07/2003] [Indexed: 10/27/2022]
Abstract
Pyridoxine 5'-phosphate oxidase catalyzes the terminal step in the synthesis of pyridoxal 5'-phosphate. The cDNA for the human enzyme has been cloned and expressed in Escherichia coli. The purified human enzyme is a homodimer that exhibits a low catalytic rate constant of approximately 0.2 sec(-1) and K(m) values in the low micromolar range for both pyridoxine 5'phosphate and pyridoxamine 5'-phosphate. Pyridoxal 5'-phosphate is an effective product inhibitor. The three-dimensional fold of the human enzyme is very similar to those of the E. coli and yeast enzymes. The human and E. coli enzymes share 39% sequence identity, but the binding sites for the tightly bound FMN and substrate are highly conserved. As observed with the E. coli enzyme, the human enzyme binds one molecule of pyridoxal 5'-phosphate tightly on each subunit.
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Affiliation(s)
- Faik N Musayev
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, VA 23219, USA
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di Salvo ML, Safo MK, Musayev FN, Bossa F, Schirch V. Structure and mechanism of Escherichia coli pyridoxine 5'-phosphate oxidase. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1647:76-82. [PMID: 12686112 DOI: 10.1016/s1570-9639(03)00060-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Escherichia coli pyridoxine 5'-phosphate oxidase (PNPOx) catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP), forming pyridoxal 5'-phosphate (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in E. coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells. Recent studies have shown that in addition to the active site, PNPOx contains a noncatalytic site that binds PLP tightly. The crystal structures of PNPOx with one and two molecules of PLP bound have been determined. In the active site, the PLP pyridine ring is stacked almost parallel against the re-face of the middle ring of flavin mononucleotide (FMN). A large protein conformational change occurs upon binding of PLP. When the protein is soaked with excess PLP an additional molecule of this cofactor is bound about 11 A from the active site. A possible tunnel exists between the two sites. Site mutants were made of all residues at the active site that make interactions with the substrate. Stereospecificity studies showed that the enzyme is specific for removal of the proR hydrogen atom from the prochiral C4' carbon of PMP. The crystal structure and the stereospecificity studies suggest that the pair of electrons on C4' of the substrate are transferred to FMN as a hydride ion.
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Affiliation(s)
- Martino L di Salvo
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università La Sapienza, P.le Aldo Moro 5, 00185, via degli Apuli 9, Rome, Italy.
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