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Parra M, Coppola M, Hellmann H. PDX proteins from Arabidopsis thaliana as novel substrates of cathepsin B: implications for vitamin B 6 biosynthesis regulation. FEBS J 2024; 291:2372-2387. [PMID: 38431778 DOI: 10.1111/febs.17110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Vitamin B6 is a critical molecule for metabolism, development, and stress sensitivity in plants. It is a cofactor for numerous biochemical reactions, can serve as an antioxidant, and has the potential to increase tolerance against both biotic and abiotic stressors. Due to the importance of vitamin B6, its biosynthesis is likely tightly regulated. Plants can synthesize vitamin B6 de novo via the concerted activity of Pyridoxine Biosynthesis Protein 1 (PDX1) and PDX2. Previously, PDX proteins have been identified as targets for ubiquitination, indicating they could be marked for degradation by two highly conserved pathways: the Ubiquitin Proteasome Pathway (UPP) and the autophagy pathway. Initial experiments show that PDXs are in fact degraded, but surprisingly, in a ubiquitin-independent manner. Inhibitor studies pointed toward cathepsin B, a conserved lysosomal cysteine protease, which is implicated in both programed cell death and autophagy in humans and plants. In plants, cathepsin Bs are poorly described, and no confirmed substrates have been identified. Here, we present PDX proteins from Arabidopsis thaliana as interactors and substrates of a plant Cathepsin B. These findings not only describe a novel cathepsin B substrate in plants, but also provide new insights into how plants regulate de novo biosynthesis of vitamin B6.
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Affiliation(s)
- Marcelina Parra
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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2
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Barra ALC, Ullah N, Brognaro H, Gutierrez RF, Wrenger C, Betzel C, Nascimento AS. Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface. J Biol Chem 2024; 300:107404. [PMID: 38782204 PMCID: PMC11237949 DOI: 10.1016/j.jbc.2024.107404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Infectious diseases are a significant cause of death, and recent studies estimate that common bacterial infectious diseases were responsible for 13.6% of all global deaths in 2019. Among the most significant bacterial pathogens is Staphylococcus aureus, accounting for more than 1.1 million deaths worldwide in 2019. Vitamin biosynthesis has been proposed as a promising target for antibacterial therapy. Here, we investigated the biochemical, structural, and dynamic properties of the enzyme complex responsible for vitamin B6 (pyridoxal 5-phosphate, PLP) biosynthesis in S. aureus, which comprises enzymes SaPdx1 and SaPdx2. The crystal structure of the 24-mer complex of SaPdx1-SaPdx2 enzymes indicated that the S. aureus PLP synthase complex forms a highly dynamic assembly with transient interaction between the enzymes. Solution scattering data indicated that SaPdx2 typically binds to SaPdx1 at a substoichiometric ratio. We propose a structure-based view of the PLP synthesis mechanism initiated with the assembly of SaPLP synthase complex that proceeds in a highly dynamic interaction between Pdx1 and Pdx2. This interface interaction can be further explored as a potentially druggable site for the design of new antibiotics.
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Affiliation(s)
- Angélica Luana C Barra
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil; Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Najeeb Ullah
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany; Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Raissa F Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany; Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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3
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Moorthy H, Yadav M, Tamang N, Mavileti SK, Singla L, Choudhury AR, Sahal D, Golakoti NR. Antiplasmodial and Antimalarial Activity of 3,5-Diarylidenetetrahydro-2H-pyran-4(3H)-ones via Inhibition of Plasmodium falciparum Pyridoxal Synthase. ChemMedChem 2023; 18:e202200411. [PMID: 36251345 DOI: 10.1002/cmdc.202200411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/13/2022] [Indexed: 01/24/2023]
Abstract
A series of 22 different 3,5-diarylidenetetrahydro-2H-pyran-4(3H)-ones (DATPs) were synthesized, characterized, and screened for their in vitro antiplasmodial activities against chloroquine (CQ)-sensitive Pf3D7, CQ-resistant PfINDO, and artemisinin-resistant PfMRA-1240 strains of Plasmodium falciparum. DATP 19 (3,5-bis(4-hydroxy-3,5-dimethoxybenzylidene)tetrahydro-2H-pyran-4(3H)-one) was found to be the most potent (IC50 1.07 μM) against PfMRA-1240, whereas 21 (3,5-bis(3,4,5-trimethoxybenzylidene)tetrahydro-2H-pyran-4(3H)-one) showed IC50 values of 1.72 and 1.44 μM against Pf3D7 and PfINDO, respectively. Resistance indices (RI) as low as 0.2 to 0.5 for 10 (3,5-bis(4-nitrobenzylidene)tetrahydro-2H-pyran-4(3H)-one) and 20 (3,5-bis(3-nitrobenzylidene)tetrahydro-2H-pyran-4(3H)-one), and <1 for most other DATPs reveals their greater potency against resistant strains than the sensitive one. The single-crystal XRD data for DATP 21 are reported. In silico support was obtained through docking studies. Killing all three strains within 4-8 h, these DATPs showed rapid kill kinetics toward the trophozoite stage. Furthermore, DATP 18 (3,5-bis(quinolin-4-ylmethylene)tetrahydro-2H-pyran-4(3H)-one) inhibited PfPdx1 enzyme activity with IC50 20.34 μM, which is about twofold lower than that (IC50 43 μM) for an already known inhibitor 4PEHz. At an oral dose of 300 mg/kg body weight, DATPs 19 and 21 were found to be nontoxic to mice, and at 100 mg/kg body weight, DATP 19 was found to suppress parasitaemia, which led to an increase in median survival time by three days relative to untreated control mice in a malaria curative study.
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Affiliation(s)
- Hariharan Moorthy
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
| | - Mamta Yadav
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Nitesh Tamang
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sai Kiran Mavileti
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
| | - Labhini Singla
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, S. A. S. Nagar, Manauli P.O., Mohali, Punjab, 140306, India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Knowledge City, Sector 81, S. A. S. Nagar, Manauli P.O., Mohali, Punjab, 140306, India
| | - Dinkar Sahal
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Nageswara Rao Golakoti
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, 515134, India
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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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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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6
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Sinthusiri A, Champasri C, Trongpanich Y. Recombinant Expression, Purification and Characterization of Pyridoxal 5'-phosphate Synthase from Geobacillus sp. H6a, Thermophilic Bacterium Producing Extracellular Vitamin B6. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2575. [PMID: 35350642 PMCID: PMC8926315 DOI: 10.30498/ijb.2021.201202.2575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background Pyridoxal 5' -phosphate synthase (PLPS) is present in deoxyxylose 5'-phosphate-independent of the de novo vitamin B6 biosynthesis pathway. This enzyme complex consists of PdxS and PdxT, which function as synthase and glutamine amidotranferase respectively to produce PLP. Objectives This study aimed to clone, express, and purify PLPS of Geobacillus sp. H6a, followed by its characterization. Material and Methods The PdxS and PdxT genes were amplified from Geobacillus (Gh) sp. H6a. Recombinant vectors pET28a-GhpdxS and pET28a-GhpdxT were constructed and the resulting His-tagged proteins were expressed in E. coli BL21(DE3). The soluble rGhpdxS and rGhpdxT were purified via nickel-affinity chromatography and cation-exchange chromatography. The mixture of rGhpdxS and rGhpdxT was further characterized. Results The molecular weights of rGhpdxS and rGhpdxT were estimated to be 35 and 23 kDa by SDS-PAGE, respectively. The native form of rGhpdxS showed hexamer and dodecamer, whereas those of rGhpdxT were a monomer upon detection with non-denaturing gel electrophoresis and gel filtration. A molar ratio of 1:1 of rGhpdxS:rGhpdxT showed the highest PLP synthesis activity (4.16 U.mg-1) and was used for analyzing the biochemical properties. The kinetic values were obtained by using glyceraldehyde 3-phosphate, ribose 5-phosphate, and glutamine as the substrates. The rGhPLPS showed pentose phosphate isomerization without triose phosphate isomerase activity. The metal ions affected PLP synthesis activity. The optimum pH and optimum temperature of rGhPLPS were 9 and 70 °C, respectively. The rGhPLPS was active over a broad range of temperatures and pH values. Conclusions These results support the potential of rGhPLPS as a candidate for industrial application.
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Affiliation(s)
| | | | - Yanee Trongpanich
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
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Barra ALC, Ullah N, Morão LG, Wrenger C, Betzel C, Nascimento AS. Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions. Front Cell Infect Microbiol 2021; 11:688380. [PMID: 34327152 PMCID: PMC8313854 DOI: 10.3389/fcimb.2021.688380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is still today one of the most concerning diseases, with 219 million infections in 2019, most of them in Sub-Saharan Africa and Latin America, causing approx. 409,000 deaths per year. Despite the tremendous advances in malaria treatment and prevention, there is still no vaccine for this disease yet available and the increasing parasite resistance to already existing drugs is becoming an alarming issue globally. In this context, several potential targets for the development of new drug candidates have been proposed and, among those, the de novo biosynthesis pathway for the B6 vitamin was identified to be a promising candidate. The reason behind its significance is the absence of the pathway in humans and its essential presence in the metabolism of major pathogenic organisms. The pathway consists of two enzymes i.e. Pdx1 (PLP synthase domain) and Pdx2 (glutaminase domain), the last constituting a transient and dynamic complex with Pdx1 as the prime player and harboring the catalytic center. In this review, we discuss the structural biology of Pdx1 and Pdx2, together with and the understanding of the PLP biosynthesis provided by the crystallographic data. We also highlight the existing evidence of the effect of PLP synthesis inhibition on parasite proliferation. The existing data provide a flourishing environment for the structure-based design and optimization of new substrate analogs that could serve as inhibitors or even suicide inhibitors.
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Affiliation(s)
- Angélica Luana C Barra
- Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil.,Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Najeeb Ullah
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Luana G Morão
- Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
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Yu P, Ma J, Zhu P, Chen Q, Zhang Q. Enhancing the production of γ-aminobutyric acid in Escherichia coli BL21 by engineering the enzymes of the regeneration pathway of the coenzyme factor pyridoxal 5'-phosphate. World J Microbiol Biotechnol 2021; 37:130. [PMID: 34236514 DOI: 10.1007/s11274-021-03103-5] [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: 03/03/2021] [Accepted: 07/02/2021] [Indexed: 11/26/2022]
Abstract
The compound γ-aminobutyric acid (GABA) was widely used in various fields. To enhance the production of GABA in Escherichia coli BL21(DE3), the enzymes of the regeneration pathway of the coenzyme factor pyridoxal 5'-phosphate (PLP) were engineered. The recombinant E. coli strain was screened and identified. The initial concentrations of L-monosodium glutamate (L-MSG) had an obvious influence on the production of GABA. The highest concentration of GABA in recombinant E. coli BL21/pET28a-gadA was 5.54 g/L when the initial L-MSG concentration was 10 g/L, whereas it was 8.45 g/L in recombinant E. coli BL21/pET28a-gadA-SNO1-SNZ1 at an initial L-MSG concentration of 15 g/L. The corresponding conversion yields of GABA in these two strains were 91.0% and 92.7%, respectively. When the initial concentrations of L-MSG were more than 15 g/L, the concentrations of GABA in E. coli BL21/pET28a-gadA-SNO1-SNZ1 were significantly higher as compared to those in recombinant E. coli BL21/pET28a-gadA, and it reached a maximum of 13.20 g/L at an initial L-MSG concentration of 25 g/L, demonstrating that the introduction of the enzymes of the regeneration pathway of PLP favored to enhance the production of GABA. This study provides new insight into producing GABA effectively in E. coli BL21(DE3).
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Affiliation(s)
- Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China.
| | - Jian Ma
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Pengzhi Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Qingwei Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Qili Zhang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
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9
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Richts B, Lentes S, Poehlein A, Daniel R, Commichau FM. A Bacillus subtilis ΔpdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:218-233. [PMID: 33559288 DOI: 10.1111/1758-2229.12936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Pyridoxal-5'-phosphate (PLP), the biologically active form of vitamin B6, serves as a cofactor for many enzymes. The Gram-positive model bacterium Bacillus subtilis synthesizes PLP via the PdxST enzyme complex, consisting of the PdxT glutaminase and the PdxS PLP synthase subunits, respectively. PdxT converts glutamine to glutamate and ammonia of which the latter is channelled to PdxS. At high extracellular ammonium concentrations, the PdxS PLP synthase subunit does not depend on PdxT. Here, we assessed the potential of a B. subtilis ΔpdxT mutant to adapt to PLP limitation at the genome level. The majority of ΔpdxT suppressors had amplified a genomic region containing the pdxS gene. We also identified mutants having acquired as yet undescribed mutations in ammonium assimilation genes, indicating that the overproduction of PdxS and the NrgA ammonium transporter partially relieve vitamin B6 limitation in a ΔpdxT mutant when extracellular ammonium is scarce. Furthermore, we found that PdxS positively affects complex colony formation in B. subtilis. The catalytic mechanism of the PdxS PLP synthase subunit could be the reason for the limited evolution of the enzyme and why we could not identify a PdxS variant producing PLP independently of PdxT at low ammonium concentrations.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Sabine Lentes
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
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10
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Richts B, Commichau FM. Underground metabolism facilitates the evolution of novel pathways for vitamin B6 biosynthesis. Appl Microbiol Biotechnol 2021; 105:2297-2305. [PMID: 33665688 PMCID: PMC7954711 DOI: 10.1007/s00253-021-11199-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 11/29/2022]
Abstract
Abstract The term vitamin B6 is a designation for the vitamers pyridoxal, pyridoxamine, pyridoxine and the respective phosphate esters pyridoxal-5′-phosphate (PLP), pyridoxamine-5′-phosphate and pyridoxine-5′-phosphate. Animals and humans are unable to synthesise vitamin B6. These organisms have to take up vitamin B6 with their diet. Therefore, vitamin B6 is of commercial interest as a food additive and for applications in the pharmaceutical industry. As yet, two naturally occurring routes for de novo synthesis of PLP are known. Both routes have been genetically engineered to obtain bacteria overproducing vitamin B6. Still, major genetic engineering efforts using the existing pathways are required for developing fermentation processes that could outcompete the chemical synthesis of vitamin B6. Recent suppressor screens using mutants of the Gram-negative and Gram-positive model bacteria Escherichia coli and Bacillus subtilis, respectively, carrying mutations in the native pathways or heterologous genes uncovered novel routes for PLP biosynthesis. These pathways consist of promiscuous enzymes and enzymes that are already involved in vitamin B6 biosynthesis. Thus, E. coli and B. subtilis contain multiple promiscuous enzymes causing a so-called underground metabolism allowing the bacteria to bypass disrupted vitamin B6 biosynthetic pathways. The suppressor screens also show the genomic plasticity of the bacteria to suppress a genetic lesion. We discuss the potential of the serendipitous pathways to serve as a starting point for the development of bacteria overproducing vitamin B6. Key points • Known vitamin B6 routes have been genetically engineered. • Underground metabolism facilitates the emergence of novel vitamin B6 biosynthetic pathways. • These pathways may be suitable to engineer bacteria overproducing vitamin B6.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Grisebachstrasse 8, 37077, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Universitätsplatz 1, 01968, Senftenberg, Germany.
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11
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Rokkam SK, Yadav M, Joshi M, Choudhury AR, Sahal D, Golakoti NR. Synthesis, in vitro anti-plasmodial potency, in-silico-cum-SPR binding with inhibition of PfPyridoxal synthase and rapid parasiticidal action by 3,5-bis{( E) arylidene}- N-methyl-4-piperidones. NEW J CHEM 2021. [DOI: 10.1039/d1nj04604g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DANMPs have been identified as new pharmacophores that have the ability to target PfPyridoxal synthase and cause rapid killing of the malaria parasite.
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Affiliation(s)
- Siva Kumar Rokkam
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
| | - Mamta Yadav
- Malaria Drug Discovery Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Mayank Joshi
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Sector 81, S. A. S. Nagar, Manauli PO, Mohali, Punjab, 140306, India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Sector 81, S. A. S. Nagar, Manauli PO, Mohali, Punjab, 140306, India
| | - Dinkar Sahal
- Malaria Drug Discovery Lab, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Nageswara Rao Golakoti
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Andhra Pradesh, India
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12
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Ullah N, Andaleeb H, Mudogo CN, Falke S, Betzel C, Wrenger C. Solution Structures and Dynamic Assembly of the 24-Meric Plasmodial Pdx1-Pdx2 Complex. Int J Mol Sci 2020; 21:ijms21175971. [PMID: 32825141 PMCID: PMC7504066 DOI: 10.3390/ijms21175971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 11/16/2022] Open
Abstract
Plasmodium species are protozoan parasites causing the deadly malaria disease. They have developed effective resistance mechanisms against most antimalarial medication, causing an urgent need to identify new antimalarial drug targets. Ideally, new drugs would be generated to specifically target the parasite with minimal or no toxicity to humans, requiring these drug targets to be distinctly different from the host’s metabolic processes or even absent in the host. In this context, the essential presence of vitamin B6 biosynthesis enzymes in Plasmodium, the pyridoxal phosphate (PLP) biosynthesis enzyme complex, and its absence in humans is recognized as a potential drug target. To characterize the PLP enzyme complex in terms of initial drug discovery investigations, we performed structural analysis of the Plasmodium vivax PLP synthase domain (Pdx1), glutaminase domain (Pdx2), and Pdx1–Pdx2 (Pdx) complex (PLP synthase complex) by utilizing complementary bioanalytical techniques, such as dynamic light scattering (DLS), X-ray solution scattering (SAXS), and electron microscopy (EM). Our investigations revealed a dodecameric Pdx1 and a monodispersed Pdx complex. Pdx2 was identified in monomeric and in different oligomeric states in solution. Interestingly, mixing oligomeric and polydisperse Pdx2 with dodecameric monodisperse Pdx1 resulted in a monodispersed Pdx complex. SAXS measurements revealed the low-resolution dodecameric structure of Pdx1, different oligomeric structures for Pdx2, and a ring-shaped dodecameric Pdx1 decorated with Pdx2, forming a heteromeric 24-meric Pdx complex.
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Affiliation(s)
- Najeeb Ullah
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a. Notkestr. 85, 22603 Hamburg, Germany; (N.U.); (H.A.); (C.N.M.); (S.F.)
- Department of Biochemistry, Bahauddin Zakariya University, Multan-60800, Punjab, Pakistan
| | - Hina Andaleeb
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a. Notkestr. 85, 22603 Hamburg, Germany; (N.U.); (H.A.); (C.N.M.); (S.F.)
- Department of Biochemistry, Bahauddin Zakariya University, Multan-60800, Punjab, Pakistan
| | - Celestin Nzanzu Mudogo
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a. Notkestr. 85, 22603 Hamburg, Germany; (N.U.); (H.A.); (C.N.M.); (S.F.)
- Department of Basic Sciences, School of Medicine, University of Kinshasa, Kinshasa BP834 KinXI, Congo
| | - Sven Falke
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a. Notkestr. 85, 22603 Hamburg, Germany; (N.U.); (H.A.); (C.N.M.); (S.F.)
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a. Notkestr. 85, 22603 Hamburg, Germany; (N.U.); (H.A.); (C.N.M.); (S.F.)
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
- Correspondence: (C.B.); (C.W.); Tel.: +49-(40)-8998-4744 (C.B.); +55-(11)-3091-7265 (C.W.)
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, 05508-000 São Paulo-SP, Brazil
- Correspondence: (C.B.); (C.W.); Tel.: +49-(40)-8998-4744 (C.B.); +55-(11)-3091-7265 (C.W.)
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Barra ALC, Dantas LDOC, Morão LG, Gutierrez RF, Polikarpov I, Wrenger C, Nascimento AS. Essential Metabolic Routes as a Way to ESKAPE From Antibiotic Resistance. Front Public Health 2020; 8:26. [PMID: 32257985 PMCID: PMC7093009 DOI: 10.3389/fpubh.2020.00026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/27/2020] [Indexed: 02/03/2023] Open
Abstract
Antibiotic resistance is a worldwide concern that requires a concerted action from physicians, patients, governmental agencies, and academia to prevent infections and the spread of resistance, track resistant bacteria, improve the use of current antibiotics, and develop new antibiotics. Despite the efforts spent so far, the current antibiotics in the market are restricted to only five general targets/pathways highlighting the need for basic research focusing on the discovery and evaluation of new potential targets. Here we interrogate two biosynthetic pathways as potentially druggable pathways in bacteria. The biosynthesis pathway for thiamine (vitamin B1), absent in humans, but found in many bacteria, including organisms in the group of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp.) and the biosynthesis pathway for pyridoxal 5'-phosphate and its vitamers (vitamin B6), found in S. aureus. Using current genomic data, we discuss the possibilities of inhibition of enzymes in the pathway and review the current state of the art in the scientific literature.
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Affiliation(s)
| | | | - Luana Galvão Morão
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Raíssa F. Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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14
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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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15
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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: 184] [Impact Index Per Article: 30.7] [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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16
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Leisico F, V Vieira D, Figueiredo TA, Silva M, Cabrita EJ, Sobral RG, Ludovice AM, Trincão J, Romão MJ, de Lencastre H, Santos-Silva T. First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD. Sci Rep 2018; 8:5313. [PMID: 29593310 PMCID: PMC5871853 DOI: 10.1038/s41598-018-22986-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/27/2018] [Indexed: 12/05/2022] Open
Abstract
Gram-positive bacteria homeostasis and antibiotic resistance mechanisms are dependent on the intricate architecture of the cell wall, where amidated peptidoglycan plays an important role. The amidation reaction is carried out by the bi-enzymatic complex MurT-GatD, for which biochemical and structural information is very scarce. In this work, we report the first crystal structure of the glutamine amidotransferase member of this complex, GatD from Staphylococcus aureus, at 1.85 Å resolution. A glutamine molecule is found close to the active site funnel, hydrogen-bonded to the conserved R128. In vitro functional studies using 1H-NMR spectroscopy showed that S. aureus MurT-GatD complex has glutaminase activity even in the absence of lipid II, the MurT substrate. In addition, we produced R128A, C94A and H189A mutants, which were totally inactive for glutamine deamidation, revealing their essential role in substrate sequestration and catalytic reaction. GatD from S. aureus and other pathogenic bacteria share high identity to enzymes involved in cobalamin biosynthesis, which can be grouped in a new sub-family of glutamine amidotransferases. Given the ubiquitous presence of GatD, these results provide significant insights into the molecular basis of the so far undisclosed amidation mechanism, contributing to the development of alternative therapeutics to fight infections.
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Affiliation(s)
- Francisco Leisico
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diana V Vieira
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Oxford Protein Production Facility, Research Complex at Harwell, Didcot, United Kingdom
| | - Teresa A Figueiredo
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal
| | - Micael Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rita G Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Madalena Ludovice
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | | | - Maria João Romão
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Microbiology of Human Pathogens Unit, Instituto de Tecnologia Química e Biológica António Xavier da Universidade Nova de Lisboa, Oeiras, Portugal.
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, USA.
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
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17
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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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18
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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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19
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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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20
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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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21
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Dietary pyridoxine controls efficacy of vitamin B6-auxotrophic tuberculosis vaccine bacillus Calmette-Guérin ΔureC::hly Δpdx1 in mice. mBio 2014; 5:e01262-14. [PMID: 24895310 PMCID: PMC4049106 DOI: 10.1128/mbio.01262-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED The only tuberculosis (TB) vaccine in use today, bacillus Calmette-Guérin (BCG), provides insufficient protection and can cause adverse events in immunocompromised individuals, such as BCGosis in HIV(+) newborns. We previously reported improved preclinical efficacy and safety of the recombinant vaccine candidate BCG ΔureC::hly, which secretes the pore-forming listeriolysin O of Listeria monocytogenes. Here, we evaluate a second-generation construct, BCG ΔureC::hly Δpdx1, which is deficient in pyridoxine synthase, an enzyme that is required for biosynthesis of the essential cofactor vitamin B6. This candidate was auxotrophic for vitamin B6 in a concentration-dependent manner, as was its survival in vivo. BCG ΔureC::hly Δpdx1 showed markedly restricted dissemination in subcutaneously vaccinated mice, which was ameliorated by dietary supplementation with vitamin B6. The construct was safer in severe combined immunodeficiency mice than the parental BCG ΔureC::hly. A prompt innate immune response to vaccination, measured by secretion of interleukin-6, granulocyte colony-stimulating factor, keratinocyte cytokine, and macrophage inflammatory protein-1α, remained independent of vitamin B6 administration, while acquired immunity, notably stimulation of antigen-specific CD4 T cells, B cells, and memory T cells, was contingent on vitamin B6 administration. The early protection provided by BCG ΔureC::hly Δpdx1 in a murine Mycobacterium tuberculosis aerosol challenge model consistently depended on vitamin B6 supplementation. Prime-boost vaccination increased protection against the canonical M. tuberculosis H37Rv laboratory strain and a clinical isolate of the Beijing/W lineage. We demonstrate that the efficacy of a profoundly attenuated recombinant BCG vaccine construct can be modulated by external administration of a small molecule. This principle fosters the development of safer vaccines required for immunocompromised individuals, notably HIV(+) infants. IMPORTANCE Mycobacterium tuberculosis can synthesize the essential cofactor vitamin B6, while humans depend on dietary supplementation. Unlike the lipophilic vitamins A, D, and E, water-soluble vitamin B6 is well tolerated at high doses. We generated a vitamin B6 auxotroph of the phase II clinical tuberculosis vaccine candidate bacillus Calmette-Guérin ΔureC::hly. The next-generation candidate was profoundly attenuated compared to the parental strain. Adaptive immunity and protection in mice consistently depended on increased dietary vitamin B6 above the daily required dose. Control of vaccine efficacy via food supplements such as vitamin B6 could provide a fast track toward improved safety. Safer vaccines are urgently needed for HIV-infected individuals at high risk of adverse events in response to live vaccines.
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22
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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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23
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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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24
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List F, Vega M, Razeto A, Häger M, Sterner R, Wilmanns M. Catalysis Uncoupling in a Glutamine Amidotransferase Bienzyme by Unblocking the Glutaminase Active Site. ACTA ACUST UNITED AC 2012; 19:1589-99. [DOI: 10.1016/j.chembiol.2012.10.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 10/02/2012] [Accepted: 10/11/2012] [Indexed: 11/30/2022]
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25
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Matsuura A, Yoon JY, Yoon HJ, Lee HH, Suh SW. Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii. Mol Cells 2012; 34:407-12. [PMID: 23104439 PMCID: PMC3887772 DOI: 10.1007/s10059-012-0198-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/04/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022] Open
Abstract
Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B(6) and is de novo synthesized from three substrates, dihydroxyacetone phosphate (DHAP), riburose 5-phosphate (RBP), and ammonia hydrolysed from glutamine. Glutamine amidotransferase (PdxT) catalyzes the production of ammonia from glutamine, while PdxS catalyzes the following condensation of ribulose 5-phosphate (Ru5P), glyceraldehyde-3-phosphate (G3P), and ammonia. PdxS exists as a hexamer or dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus horikoshii PdxS has a 37 amino acids insertion region, which is found in some archaeal PdxS proteins, but its structure and function are unknown. To provide further structural information on the role of the insertion region, the oligomeric state, and ligand binding mode of P. horikoshii PdxS, the crystal structure of PdxS from P. horikoshii was solved in two forms: (i) apo form, (ii) r ibose 5-phosphate (R5P) complex and the quaternary structure of PdxS in solution was determined by analytical gel filtration. P. horikoshii PdxS forms hexamer in solution based on analytical gel filtration data. When we superimpose the structure of P. horikoshii PdxS with other dodecamer structures of PdxS, the additional insertion is located apart from the active site and induces a steric clash on the hexamer-hexamer interface of PdxS proteins. Our results suggest that the additional insertion perturbs dodecamer formation of P. horikoshii PdxS.
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Affiliation(s)
- Atsushi Matsuura
- Department of Bio & Nano Chemistry, Kookmin University, Seoul 136-702,
Korea
| | - Ji Young Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742,
Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742,
Korea
| | - Hyung Ho Lee
- Department of Bio & Nano Chemistry, Kookmin University, Seoul 136-702,
Korea
- Department of Integrative Biomedical Science and Engineering, Kookmin University, Seoul 136-702,
Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742,
Korea
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742,
Korea
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