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Thaker K, Patoliya J, Rabadiya K, Patel D, Ponnuchamy M, Rama Reddy NR, Joshi R. An in-silico approach to unravel the structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS): a critical enzyme for sennoside biosynthesis in Cassia angustifolia Vahl. J Biomol Struct Dyn 2024; 42:3848-3861. [PMID: 37243697 DOI: 10.1080/07391102.2023.2216300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 05/13/2023] [Indexed: 05/29/2023]
Abstract
The laxative properties of senna are attributed to the presence of sennosides produced in the plant. The low production level of sennosides in the plant is an important impediment to their growing demand and utilization. Understanding biosynthetic pathways helps to engineer them in terms of enhanced production. The biosynthetic pathways of sennoside production in plants are not completely known yet. However, attempts to get information on genes and proteins engaged in it have been made which decode involvement of various pathways including shikimate pathway. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAHPS) is a key enzyme involved in sennosides production through the shikimate pathway. Unfortunately, there is no information available on proteomic characterization of DAHPS enzyme of senna (caDAHPS) resulting in lack of knowledge about its role. We for the first time characterized DAHPS enzyme of senna using in-silico analysis. To the best of our knowledge this is the first attempt to identify the coding sequence of caDAHPS by cloning and sequencing. We found Gln179, Arg175, Glu462, Glu302, Lys357 and His420 amino acids in the active site of caDAHPS through molecular docking. followed by molecular dynamic simulation. The amino acid residues, Lys182, Cys136, His460, Leu304, Gly333, Glu334, Pro183, Asp492 and Arg433 at the surface interact with PEP by van der Waals bonds imparting stability to the enzyme-substrate complex. Docking results were further validated by molecular dynamics. The presented in-silico analysis of caDAHPS will generate opportunities to engineer the sennoside biosynthesis in plants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khushali Thaker
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Jaimini Patoliya
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Khushbu Rabadiya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Dhaval Patel
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Manivel Ponnuchamy
- ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat, India
| | | | - Rushikesh Joshi
- Department of Biochemistry & Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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Kanaris M, Poulin J, Shahinas D, Johnson D, Crowley VM, Fucile G, Provart N, Christendat D. Elevated tyrosine results in the cytosolic retention of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:789-803. [PMID: 34797933 DOI: 10.1111/tpj.15590] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
The shikimate pathway plays a central role in the biosynthesis of aromatic amino acids and specialized metabolites in plants. The first enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAHPS) serves as a key regulatory point for the pathway in various organisms. These enzymes are important in regulating the shikimate pathway in multiple microbial systems. The mechanism of regulation of DAHPS is poorly understood in plants, and the role of tyrosine (Tyr) with respect to the three DAHPS isozymes from Arabidopsis thaliana was investigated. In vitro enzymatic analyses established that Tyr does not function as an allosteric regulator for the A. thaliana DAHPS isozymes. In contrast, Arabidopsis T-DNA insertional mutants for the DAHPS1 locus, dahps1, are hypersensitive to elevated Tyr. Tyr hypersensitivity can be reversed with tryptophan and phenylalanine supplementation, indicating that Tyr is affecting the shikimate pathway flux in the dahps1 mutant. Tyr treatment of Arabidopsis seedlings showed reduced accumulation of overexpressed DAHPS2 in the chloroplast. Further, bimolecular fluorescence complementation studies revealed that DAHPS2 interacts with a 14-3-3 protein in the cytosol, and this interaction is enhanced with Tyr treatment. This interaction with 14-3-3 may retain DAHPS2 in the cytosol, which prevents its ability to function in the chloroplast with elevated Tyr.
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Affiliation(s)
- Michael Kanaris
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Jimmy Poulin
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Dea Shahinas
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Daniel Johnson
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Valerie M Crowley
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Geoffrey Fucile
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
- Center for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B, Canada
- Center for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
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Gruenberg M, Irla M, Myllek S, Draths K. Characterization of two 3-deoxy-d-Arabino-Heptulosonate 7-phosphate synthases from Bacillusmethanolicus. Protein Expr Purif 2021; 188:105972. [PMID: 34517109 DOI: 10.1016/j.pep.2021.105972] [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: 06/28/2021] [Revised: 08/23/2021] [Accepted: 09/07/2021] [Indexed: 10/20/2022]
Abstract
3-Deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase catalyzes the condensation of phosphoenolpyruvate (PEP) with d-erythrose 4-phosphate (E4P) and plays an important role in regulating carbon flux toward aromatic amino acid biosynthesis in bacteria and plants. Sequence analysis of the DAHP synthases AroG1 and AroG2 from Bacillus methanolicus MGA3 suggested this thermophilic, methylotrophic bacterium possesses two type Iβ DAHP synthases. This study describes production of AroG1 and AroG2 in Escherichia coli as hexa-histidine fused proteins, which were purified by affinity chromatography. Treatment with TEV protease afforded native proteins for characterization and kinetic analysis. AroG1 and AroG2 are, respectively, 30.1 kDa and 40.0 kDa proteins. Both enzymes have maximal activity over a pH range of 6.3-7.2. The apparent kinetic parameters at 50 °C and pH 7.2 for AroG1 are KmPEP 1100 ± 100 μM, KmE4P 530 ± 100 μM, and kcat 10.3 ± 1.2 s-1. The kinetic parameters for AroG2 are KmPEP 90 ± 20 μM, KmE4P 130 ± 40 μM, and kcat 2.0 ± 0.2 s-1. At 50 °C AroG2 retains 50% of its activity after 96 min whereas AroG1 retains less than 5% of its activity after 10 min. AroG2, which contains an N-terminal regulatory domain, is inhibited by chorismate and prephenate but not l-phenylalanine, l-tyrosine, or l-tryptophan. AroG1 is not inhibited by any of the molecules examined. Understanding DAHP synthase regulation in B. methanolicus is a first step toward generating biocatalysts that exploit the target-rich aromatic amino acid biosynthetic pathway for synthesis of chemicals from methanol.
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Affiliation(s)
- Megan Gruenberg
- Department of Chemistry, 578 S. Shaw Lane, Michigan State University, East Lansing, MI, 48824, USA.
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7034 Trondheim, Norway.
| | - Sebastian Myllek
- Department of Chemistry, 578 S. Shaw Lane, Michigan State University, East Lansing, MI, 48824, USA.
| | - Karen Draths
- Department of Chemistry, 578 S. Shaw Lane, Michigan State University, East Lansing, MI, 48824, USA.
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The TK0271 Protein Activates Transcription of Aromatic Amino Acid Biosynthesis Genes in the Hyperthermophilic Archaeon Thermococcus kodakarensis. mBio 2019; 10:mBio.01213-19. [PMID: 31506306 PMCID: PMC6737238 DOI: 10.1128/mbio.01213-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanisms of transcriptional regulation in archaea are still poorly understood. In this study, we identified a transcriptional regulator in the hyperthermophilic archaeon Thermococcus kodakarensis that activates the transcription of three operons involved in the biosynthesis of aromatic amino acids. The study represents one of only a few that identifies a regulator in Archaea that activates transcription. The results also imply that transcriptional regulation of genes with the same function is carried out by diverse mechanisms in the archaea, depending on the lineage. TrpY from Methanothermobacter thermautotrophicus is a regulator that inhibits transcription of the Trp biosynthesis (trp) operon. Here, we show that the TrpY homolog in Thermococcus kodakarensis is not involved in such regulation. There are 87 genes on the T. kodakarensis genome predicted to encode transcriptional regulators (TRs). By screening for TRs that specifically bind to the promoter of the trp operon of T. kodakarensis, we identified TK0271. The gene resides in the aro operon, responsible for the biosynthesis of chorismate, a precursor for Trp, Tyr, and Phe. TK0271 was expressed in Escherichia coli, and the protein, here designated Tar (Thermococcalesaromatic amino acid regulator), was purified. Tar specifically bound to the trp promoter with a dissociation constant (Kd) value of approximately 5 nM. Tar also bound to the promoters of the Tyr/Phe biosynthesis (tyr-phe) and aro operons. The protein recognized a palindromic sequence (TGGACA-N8-TGTCCA) conserved in these promoters. In vitro transcription assays indicated that Tar activates transcription from all three promoters. We cultivated T. kodakarensis in amino acid-based medium and found that transcript levels of the trp, tyr-phe, and aro operons increased in the absence of Trp, Tyr, or Phe. We further constructed a TK0271 gene disruption strain (ΔTK0271). Growth of ΔTK0271 was similar to that of the host strain in medium including Trp, Tyr, and Phe but was significantly impaired in the absence of any one of these amino acids. The results suggest that Tar is responsible for the transcriptional activation of aromatic amino acid biosynthesis genes in T. kodakarensis.
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Zhao H, Gao H, Ji K, Yan B, Li Q, Mo S, Zheng M, Ou Q, Wu B, Li N, Jiang C. Isolation and biochemical characterization of a metagenome-derived 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase gene from subtropical marine mangrove wetland sediments. AMB Express 2019; 9:19. [PMID: 30715617 PMCID: PMC6362186 DOI: 10.1186/s13568-019-0742-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/23/2019] [Indexed: 11/10/2022] Open
Abstract
3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key rate-limiting enzyme in aromatic amino acid anabolism. A new Iβ-type DAHPS gene (aro1A) was identified in a metagenomic library from subtropical marine mangrove sediment. The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level. Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (β/α)8 barrel-shaped catalytic structural domain of DAHPS. The motifs and amino acid residues involved in the combination of substrates and metal ligand were highly conservative with the known DAHPS. The putative DAHPS gene was subcloned into a pET-30a(+) vector and was overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein was purified to homogeneity. The maximum activity for the recombinant Aro1A protein occurred at pH 8.0 and 40 °C. Ba2+ and Ca2+ stimulated the activity of Aro1A protein. The enzyme showed high affinity and catalytic efficiency (K m PEP = 19.58 μM, V max PEP = 29.02 μM min-1, and k cat PEP /K m PEP = 0.88 s-1 μM-1) under optimal reaction conditions. The enzymatic property of Aro1A indicates its potential in aromatic amino acid industrial production.
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Affiliation(s)
- Huaxian Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Hua Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Kai Ji
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Bing Yan
- Guangxi Key Laboratory of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, 92 Changqing Road, Beihai, 536000 Guangxi People’s Republic of China
| | - Quanwen Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Minggang Zheng
- The First Institute of Oceanography, State Oceanic Administration of China, 6 XianXiaLing Road, Qingdao, 266061 People’s Republic of China
| | - Qian Ou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Bo Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
| | - Nan Li
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Guangxi Teachers Education University), Ministry of Education, 175 Mingxiu East Road, Nanning, 530001 Guangxi People’s Republic of China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue East Road, Nanning, 530004 Guangxi People’s Republic of China
- Guangxi Key Laboratory of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, 92 Changqing Road, Beihai, 536000 Guangxi People’s Republic of China
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6
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Bai Y, Lang EJM, Nazmi AR, Parker EJ. Domain cross-talk within a bifunctional enzyme provides catalytic and allosteric functionality in the biosynthesis of aromatic amino acids. J Biol Chem 2019; 294:4828-4842. [PMID: 30670586 DOI: 10.1074/jbc.ra118.005220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
Because of their special organization, multifunctional enzymes play crucial roles in improving the performance of metabolic pathways. For example, the bacterium Prevotella nigrescens contains a distinctive bifunctional protein comprising a 3-deoxy-d-arabino heptulosonate-7-phosphate synthase (DAH7PS), catalyzing the first reaction of the biosynthetic pathway of aromatic amino acids, and a chorismate mutase (CM), functioning at a branch of this pathway leading to the synthesis of tyrosine and phenylalanine. In this study, we characterized this P. nigrescens enzyme and found that its two catalytic activities exhibit substantial hetero-interdependence and that the separation of its two distinct catalytic domains results in a dramatic loss of both DAH7PS and CM activities. The protein displayed a unique dimeric assembly, with dimerization solely via the CM domain. Small angle X-ray scattering (SAXS)-based structural analysis of this protein indicated a DAH7PS-CM hetero-interaction between the DAH7PS and CM domains, unlike the homo-association between DAH7PS domains normally observed for other DAH7PS proteins. This hetero-interaction provides a structural basis for the functional interdependence between the two domains observed here. Moreover, we observed that DAH7PS is allosterically inhibited by prephenate, the product of the CM-catalyzed reaction. This allostery was accompanied by a striking conformational change as observed by SAXS, implying that altering the hetero-domain interaction underpins the allosteric inhibition. We conclude that for this C-terminal CM-linked DAH7PS, catalytic function and allosteric regulation appear to be delivered by a common mechanism, revealing a distinct and efficient evolutionary strategy to utilize the functional advantages of a bifunctional enzyme.
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Affiliation(s)
- Yu Bai
- From the Maurice Wilkins Centre, Ferrier Research Institute, Victoria University of Wellington, Wellington 6012 and
| | - Eric J M Lang
- the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand
| | - Ali Reza Nazmi
- the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand
| | - Emily J Parker
- From the Maurice Wilkins Centre, Ferrier Research Institute, Victoria University of Wellington, Wellington 6012 and .,the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch 8041, New Zealand
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Structural and functional characterisation of the entry point to pyocyanin biosynthesis in Pseudomonas aeruginosa defines a new 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase subclass. Biosci Rep 2018; 38:BSR20181605. [PMID: 30242059 PMCID: PMC6435475 DOI: 10.1042/bsr20181605] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/17/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022] Open
Abstract
In Pseudomonas aeruginosa (Pae), the shikimate pathway end product, chorismate, serves as the last common precursor for the biosynthesis of both primary aromatic metabolites, including phenylalanine, tyrosine and tryptophan, and secondary aromatic metabolites, including phenazine-1-carboxylic acid (PCA) and pyocyanin (PYO). The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first committed step of the shikimate pathway, en route to chorismate. P. aeruginosa expresses multiple, distinct DAH7PSs that are associated with either primary or secondary aromatic compound biosynthesis. Here we report the structure of a type II DAH7PS, encoded by phzC as part of the duplicated phenazine biosynthetic cluster, from P. aeruginosa (PAO1) revealing for the first time the structure of a type II DAH7PS involved in secondary metabolism. The omission of the structural elements α2a and α2b, relative to other characterised type II DAH7PSs, leads to the formation of an alternative, dimeric, solution-state structure for this type II DAH7PS with an oligomeric interface that has not previously been characterised and that does not facilitate the formation of aromatic amino acid allosteric binding sites. The sequence similarity and, in particular, the common N-terminal extension suggest a common origin for the type II DAH7PSs from P. aeruginosa. The results described in the present study support an expanded classification of the type II DAH7PSs as type IIA and type IIB based on sequence characteristics, structure and function of the resultant proteins, and on defined physiological roles within primary or secondary metabolism.
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Sharma A, Kumar V, Chatrath A, Dev A, Prasad R, Sharma AK, Tomar S, Kumar P. In vitro metal catalyzed oxidative stress in DAH7PS: Methionine modification leads to structure destabilization and induce amorphous aggregation. Int J Biol Macromol 2018; 106:1089-1106. [DOI: 10.1016/j.ijbiomac.2017.08.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 11/28/2022]
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Nazmi AR, Lang EJM, Bai Y, Allison TM, Othman MH, Panjikar S, Arcus VL, Parker EJ. Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate. J Biol Chem 2016; 291:21836-21847. [PMID: 27502275 DOI: 10.1074/jbc.m116.741637] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multifunctional proteins play a variety of roles in metabolism. Here, we examine the catalytic function of the combined 3-deoxy-d-arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM) from Geobacillus sp. DAH7PS operates at the start of the biosynthetic pathway for aromatic metabolites, whereas CM operates in a dedicated branch of the pathway for the biosynthesis of amino acids tyrosine and phenylalanine. In line with sequence predictions, the two catalytic functions are located in distinct domains, and these two activities can be separated and retain functionality. For the full-length protein, prephenate, the product of the CM reaction, acts as an allosteric inhibitor for the DAH7PS. The crystal structure of the full-length protein with prephenate bound and the accompanying small angle x-ray scattering data reveal the molecular mechanism of the allostery. Prephenate binding results in the tighter association between the dimeric CM domains and the tetrameric DAH7PS, occluding the active site and therefore disrupting DAH7PS function. Acquisition of a physical gating mechanism to control catalytic function through gene fusion appears to be a general mechanism for providing allostery for this enzyme.
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Affiliation(s)
- Ali Reza Nazmi
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Eric J M Lang
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Yu Bai
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Timothy M Allison
- the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 5QY, United Kingdom
| | - Mohamad H Othman
- From the Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Santosh Panjikar
- the Australian Synchrotron, Clayton, Melbourne, Victoria 3168, Australia.,the Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Vickery L Arcus
- the School of Science, University of Waikato, Hamilton 3240, New Zealand, and
| | - Emily J Parker
- the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
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Inhibition of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis: in silico screening and in vitro validation. Eur J Med Chem 2015; 105:182-93. [PMID: 26491981 DOI: 10.1016/j.ejmech.2015.10.014] [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] [Received: 08/28/2015] [Revised: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 11/20/2022]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, remains a serious global health threat, highlighting the urgent need for novel antituberculosis drugs. The shikimate pathway, responsible for aromatic amino acid biosynthesis, is required for the growth of Mycobacterium tuberculosis and is a potential drug target. 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (mtDAH7Ps) catalyzes the first step in shikimate pathway. E-pharmacophore models for inhibitors of mtDAH7Ps - tyrosine, phenylalanine, phosphoenolpyruvate and (2S)-2,7-bis(phosphonooxy)heptanoic acid were screened against ZINC synthetic and natural compounds databases. The shortlisted compounds were subjected to induce fit docking and validated by Prime/Molecular Mechanics Generalized Born Surface Area calculation to predict ligand binding energy and ligand strain energy for ligand and receptor. The lead compounds were screened for their inhibitory activity against purified mtDAH7Ps enzyme. Lead compounds inhibited mtDAH7Ps in a concentration-dependent manner; with an IC50 value of 21 μM, 42 μM and 54 μM for α-Tocopherol, rutin and 3-Pyridine carboxyaldehyde respectively. Molecular Dynamics analysis for 50 ns of the active compounds-mtDAH7Ps complexes showed that the backbone of mtDAH7Ps was stable. These results suggest that α-tocopherol, 3 - Pyridine carboxyaldehyde and rutin could be novel drug leads to inhibit mtDAH7Ps in M. tuberculosis.
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Bains W, Xiao Y, Yu C. Prediction of the maximum temperature for life based on the stability of metabolites to decomposition in water. Life (Basel) 2015; 5:1054-100. [PMID: 25821932 PMCID: PMC4500130 DOI: 10.3390/life5021054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/03/2015] [Accepted: 03/05/2015] [Indexed: 12/01/2022] Open
Abstract
The components of life must survive in a cell long enough to perform their function in that cell. Because the rate of attack by water increases with temperature, we can, in principle, predict a maximum temperature above which an active terrestrial metabolism cannot function by analysis of the decomposition rates of the components of life, and comparison of those rates with the metabolites' minimum metabolic half-lives. The present study is a first step in this direction, providing an analytical framework and method, and analyzing the stability of 63 small molecule metabolites based on literature data. Assuming that attack by water follows a first order rate equation, we extracted decomposition rate constants from literature data and estimated their statistical reliability. The resulting rate equations were then used to give a measure of confidence in the half-life of the metabolite concerned at different temperatures. There is little reliable data on metabolite decomposition or hydrolysis rates in the literature, the data is mostly confined to a small number of classes of chemicals, and the data available are sometimes mutually contradictory because of varying reaction conditions. However, a preliminary analysis suggests that terrestrial biochemistry is limited to environments below ~150-180 °C. We comment briefly on why pressure is likely to have a small effect on this.
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Affiliation(s)
- William Bains
- Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Avenue, Cambridge, MA 02139, USA.
| | - Yao Xiao
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.
| | - Changyong Yu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.
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Nazmi AR, Schofield LR, Dobson RC, Jameson GB, Parker EJ. Destabilization of the Homotetrameric Assembly of 3-Deoxy-d-Arabino-Heptulosonate-7-Phosphate Synthase from the Hyperthermophile Pyrococcus furiosus Enhances Enzymatic Activity. J Mol Biol 2014; 426:656-73. [DOI: 10.1016/j.jmb.2013.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/05/2013] [Accepted: 11/06/2013] [Indexed: 12/30/2022]
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13
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Cross PJ, Pietersma AL, Allison TM, Wilson-Coutts SM, Cochrane FC, Parker EJ. Neisseria meningitidis expresses a single 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase that is inhibited primarily by phenylalanine. Protein Sci 2013; 22:1087-99. [PMID: 23754471 DOI: 10.1002/pro.2293] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/26/2013] [Accepted: 05/28/2013] [Indexed: 11/12/2022]
Abstract
Neisseria meningitidis is the causative agent of meningitis and meningococcal septicemia is a major cause of disease worldwide, resulting in brain damage and hearing loss, and can be fatal in a large proportion of cases. The enzyme 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyzes the first reaction in the shikimate pathway leading to the biosynthesis of aromatic metabolites including the aromatic acids l-Trp, l-Phe, and l-Tyr. This pathway is absent in humans, meaning that enzymes of the pathway are considered as potential candidates for therapeutic intervention. As the entry point, feedback inhibition of DAH7PS by pathway end products is a key mechanism for the control of pathway flux. The structure of the single DAH7PS expressed by N. meningitidis was determined at 2.0 Å resolution. In contrast to the other DAH7PS enzymes, which are inhibited only by a single aromatic amino acid, the N. meningitidis DAH7PS was inhibited by all three aromatic amino acids, showing greatest sensitivity to l-Phe. An N. meningitidis enzyme variant, in which a single Ser residue at the bottom of the inhibitor-binding cavity was substituted to Gly, altered inhibitor specificity from l-Phe to l-Tyr. Comparison of the crystal structures of both unbound and Tyr-bound forms and the small angle X-ray scattering profiles reveal that N. meningtidis DAH7PS undergoes no significant conformational change on inhibitor binding. These observations are consistent with an allosteric response arising from changes in protein motion rather than conformation, and suggest ligands that modulate protein dynamics may be effective inhibitors of this enzyme.
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Affiliation(s)
- Penelope J Cross
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
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14
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Engineering allosteric control to an unregulated enzyme by transfer of a regulatory domain. Proc Natl Acad Sci U S A 2013; 110:2111-6. [PMID: 23345433 DOI: 10.1073/pnas.1217923110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allosteric regulation of protein function is a critical component of metabolic control. Its importance is underpinned by the diversity of mechanisms and its presence in all three domains of life. The first enzyme of the aromatic amino acid biosynthesis, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, shows remarkable variation in allosteric response and machinery, and both contemporary regulated and unregulated orthologs have been described. To examine the molecular events by which allostery can evolve, we have generated a chimeric protein by joining the catalytic domain of an unregulated 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with the regulatory domain of a regulated enzyme. We demonstrate that this simple gene fusion event on its own is sufficient to confer functional allostery to the unregulated enzyme. The fusion protein shares structural similarities with its regulated parent protein and undergoes an analogous major conformational change in response to the binding of allosteric effector tyrosine to the regulatory domain. These findings help delineate a remarkably facile mechanism for the evolution of modular allostery by domain recruitment.
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15
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Tran D, Pietersma AL, Schofield LR, Rost M, Jameson GB, Parker EJ. Investigating the role of the hydroxyl groups of substrate erythrose 4-phosphate in the reaction catalysed by the first enzyme of the shikimate pathway. Bioorg Med Chem Lett 2011; 21:6838-41. [PMID: 21978677 DOI: 10.1016/j.bmcl.2011.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/04/2011] [Accepted: 09/06/2011] [Indexed: 11/28/2022]
Abstract
3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) synthase catalyses the first step of the shikimate pathway, which is responsible for the biosynthesis of aromatic amino acids in microorganisms and plants. This enzyme catalyses an aldol reaction between phosphoenolpyruvate and D-erythrose 4-phosphate to generate DAH7P. Both 2-deoxyerythrose 4-phosphate and 3-deoxyerythrose 4-phosphate were synthesised and tested as alternative substrates for the enzyme. Both compounds were found to be substrates for the DAH7P synthases from Escherichia coli, Pyrococcus furiosus and Mycobacterium tuberculosis, consistent with an acyclic mechanism for the enzyme for which neither C2 nor C3 hydroxyl groups are required for catalysis. The enzymes all showed greater tolerance for the loss of the C2 hydroxyl group than the C3 hydroxyl group.
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Affiliation(s)
- David Tran
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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16
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Zhou L, Wu J, Vijayalakshmi J, Shumilin IA, Bauerle R, Kretsinger RH, Woodard RW. Structure and characterization of the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Aeropyrum pernix. Bioorg Chem 2011; 40:79-86. [PMID: 22035970 DOI: 10.1016/j.bioorg.2011.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/07/2011] [Accepted: 09/08/2011] [Indexed: 11/18/2022]
Abstract
The first enzyme in the shikimic acid biosynthetic pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), varies significantly in size and complexity in the bacteria and plants that express it. The DAH7PS from the archaebacterium Aeropyrum pernix (DAH7PS(Ap)) is among the smallest and least complex of the DAH7PS enzymes, leading to the hypothesis that DAH7PS(Ap) would not be subject to feedback regulation by shikimic acid pathway products. We overexpressed DAH7PS(Ap) in Escherichia coli, purified it, and characterized its enzymatic activity. We then solved its X-ray crystal structure with a divalent manganese ion and phosphoenolpyruvate bound (PDB ID: 1VS1). DAH7PS(Ap) is a homodimeric metalloenzyme in solution. Its enzymatic activity increases dramatically above 60 °C, with optimum activity at 95 °C. Its pH optimum at 60 °C is 5.7. DAH7PS(Ap) follows Michaelis-Menten kinetics at 60 °C, with a K(M) for erythrose 4-phosphate of 280 μM, a K(M) for phosphoenolpyruvate of 891 μM, and a k(cat) of 1.0 s(-1). None of the downstream products of the shikimate biosynthetic pathway we tested inhibited the activity of DAH7PS(Ap). The structure of DAH7PS(Ap) is similar to the structures of DAH7PS from Thermatoga maritima (PDB ID: 3PG8) and Pyrococcus furiosus (PDB ID: 1ZCO), and is consistent with its designation as an unregulated DAH7PS.
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Affiliation(s)
- Lily Zhou
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States.
| | - Jing Wu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States.
| | - J Vijayalakshmi
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States
| | - Igor A Shumilin
- Department of Biology, University of Virginia, Charlottesville, VA 22903, United States.
| | - Ronald Bauerle
- Department of Biology, University of Virginia, Charlottesville, VA 22903, United States.
| | - Robert H Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA 22903, United States.
| | - Ronald W Woodard
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48105-1065, United States.
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17
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Cross PJ, Dobson RCJ, Patchett ML, Parker EJ. Tyrosine latching of a regulatory gate affords allosteric control of aromatic amino acid biosynthesis. J Biol Chem 2011; 286:10216-24. [PMID: 21282100 DOI: 10.1074/jbc.m110.209924] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The first step of the shikimate pathway for aromatic amino acid biosynthesis is catalyzed by 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS). Thermotoga maritima DAH7PS (TmaDAH7PS) is tetrameric, with monomer units comprised of a core catalytic (β/α)(8) barrel and an N-terminal domain. This enzyme is inhibited strongly by tyrosine and to a lesser extent by the presence of phenylalanine. A truncated mutant of TmaDAH7PS lacking the N-terminal domain was catalytically more active and completely insensitive to tyrosine and phenylalanine, consistent with a role for this domain in allosteric inhibition. The structure of this protein was determined to 2.0 Å. In contrast to the wild-type enzyme, this enzyme is dimeric. Wild-type TmaDAH7PS was co-crystallized with tyrosine, and the structure of this complex was determined to a resolution of 2.35 Å. Tyrosine was found to bind at the interface between two regulatory N-terminal domains, formed from diagonally located monomers of the tetramer, revealing a major reorganization of the regulatory domain with respect to the barrel relative to unliganded enzyme. This significant conformational rearrangement observed in the crystal structures was also clearly evident from small angle X-ray scattering measurements recorded in the presence and absence of tyrosine. The closed conformation adopted by the protein on tyrosine binding impedes substrate entry into the neighboring barrel, revealing an unusual tyrosine-controlled gating mechanism for allosteric control of this enzyme.
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Affiliation(s)
- Penelope J Cross
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8040, New Zealand
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18
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Effective solubilization and single-step purification of Bacillus licheniformis alpha-amylase from insoluble aggregates. Folia Microbiol (Praha) 2010; 55:133-6. [PMID: 20490755 DOI: 10.1007/s12223-010-0020-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 10/22/2009] [Indexed: 10/19/2022]
Abstract
A high level expression of thermostable alpha-amylase gene from Bacillus licheniformis in Escherichia coli was obtained. The recombinant enzyme was mainly produced in the form of insoluble aggregates. The enzyme was solubilized without using denaturing agents and purified to homogeneity in a single step by ion exchange chromatography. The enzyme was purified 138-fold with a final yield of 349 %; the specific activity of the purified enzyme was 1343 U/mg.
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19
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Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature 2010; 464:1077-81. [PMID: 20348906 DOI: 10.1038/nature08884] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 02/05/2010] [Indexed: 11/08/2022]
Abstract
Most archaeal groups and deeply branching bacterial lineages harbour thermophilic organisms with a chemolithoautotrophic metabolism. They live at high temperatures in volcanic habitats at the expense of inorganic substances, often under anoxic conditions. These autotrophic organisms use diverse carbon dioxide fixation mechanisms generating acetyl-coenzyme A, from which gluconeogenesis must start. Here we show that virtually all archaeal groups as well as the deeply branching bacterial lineages contain a bifunctional fructose 1,6-bisphosphate (FBP) aldolase/phosphatase with both FBP aldolase and FBP phosphatase activity. This enzyme is missing in most other Bacteria and in Eukaryota, and is heat-stabile even in mesophilic marine Crenarchaeota. Its bifunctionality ensures that heat-labile triosephosphates are quickly removed and trapped in stabile fructose 6-phosphate, rendering gluconeogenesis unidirectional. We propose that this highly conserved, heat-stabile and bifunctional FBP aldolase/phosphatase represents the pace-making ancestral gluconeogenic enzyme, and that in evolution gluconeogenesis preceded glycolysis.
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20
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Wang L, Zhou Q, Chen H, Chu Z, Lu J, Zhang Y, Yang S. Efficient solubilization, purification of recombinant extracellular α-amylase from pyrococcus furiosus expressed as inclusion bodies in Escherichia coli. J Ind Microbiol Biotechnol 2006; 34:187-92. [PMID: 17119903 DOI: 10.1007/s10295-006-0185-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 10/25/2006] [Indexed: 11/30/2022]
Abstract
The gene encoding the Pyrococcus furiosus extracellular alpha-amylase (PFA) was amplified by PCR from P. furiosus genomic DNA and was highly expressed in Escherichia coli BL21-Codon Plus (DE3)-RIL. The recombinant alpha-amylase was mainly expressed in the form of insoluble inclusion bodies. An improved purification method was established in this paper. The solubilization of the inclusion bodies was achieved by 90 degrees C treatment for 3 min in Britton-Robinson buffer at pH 10.5. The solubilized PFA was then diluted and subsequently purified by Phenyl Sepharose chromatography. The overall yield of the new purification method was about 58,000 U/g wet cells, which is higher than previously reported.
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Affiliation(s)
- Lisa Wang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Science, 500 Caobao Road, 200233 Shanghai, China
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21
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Koma D, Sawai T, Harayama S, Kino K. Overexpression of the genes from thermophiles in Escherichia coli by high-temperature cultivation. Appl Microbiol Biotechnol 2006; 73:172-80. [PMID: 16652221 DOI: 10.1007/s00253-006-0448-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 03/25/2006] [Accepted: 03/28/2006] [Indexed: 12/18/2022]
Abstract
Twenty-nine aminotransferase genes from Pyrococcus horikoshii, Aeropyrum pernix, and Sulfolobus tokodaii were cloned and expressed in Escherichia coli. The expression of several of the genes at 15, 25, or 37 degrees C resulted in the formation of insoluble protein aggregates. Therefore, we developed a simple method to express these genes into soluble proteins, by cultivating E. coli clones at a higher temperature. Thus, four genes could be expressed efficiently into soluble and active enzymes by cultivating the respective E. coli clones at 46 degrees C. Subsequently, the method was applied to the expression into soluble proteins of other aminotransferase genes that were derived from nine species of thermophilic microorganisms.
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Affiliation(s)
- Daisuke Koma
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0812, Japan.
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22
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Wu J, Sheflyan G, Woodard R. Bacillus subtilis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase revisited: resolution of two long-standing enigmas. Biochem J 2006; 390:583-90. [PMID: 15869469 PMCID: PMC1198938 DOI: 10.1042/bj20050294] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mono/bifunctional and metallo/non-metallo properties of Bacillus subtilis DAHPS (3-deoxy-D-arabino-heptulosonate 7-phosphate synthase) have been controversial for several decades. The present study investigated the DAHPSs from both the B. subtilis parent Marburg strain and the derivative strain 168 in detail and clarified the above two long-standing questions. The DAHPSs from the parent and the derivative 168 strains have identical sequence and are both bifunctional enzymes with a CM (chorismate mutase) activity and a DAHPS activity. The parent strain expresses a second independent monofunctional CM, encoded by aroH, that is highly active, while the 168 strain expresses an aroH containing a single residue mutation (A112V) that is significantly less active thus leading to previous confusion regarding the mono/bifunctionality of DAHPS. Metal analysis showed that B. subtilis DAHPS as isolated contained iron and zinc and is inactivated by dipicolinic acid; the inactive apoenzyme can be reactivated by bivalent metal ions, indicating that the enzyme is a metalloenzyme. The enzyme-bound metal is insensitive to EDTA treatment, leading to the previous conclusion that this DAHPS does not require a metal. The enzyme displays a homotetrameric structure in solution and appears to follow Michaelis-Menten kinetics with K(m)(PEP)=139+/-11.4 microM for phosphoenolpyruvate, K(m)(E4P)=1760+/-110 microM for D-erythrose 4-phosphate, kcat=4.6+/-0.1 s(-1) for DAHPS activity and K(m)(chorismate)=850+/-97 microM, kcat=0.41+/-0.01 s(-1) for CM activity. B. subtilis DAHPS is inhibited by the Shikimate pathway intermediates prephenate and chorismate.
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Affiliation(s)
- Jing Wu
- Department of Medicinal Chemistry and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, U.S.A
| | - Galina Ya. Sheflyan
- Department of Medicinal Chemistry and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, U.S.A
| | - Ronald W. Woodard
- Department of Medicinal Chemistry and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, U.S.A
- To whom correspondence should be addressed, at College of Pharmacy, 428 Church St., Ann Arbor, MI 48109-1065, U.S.A. (email )
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23
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Wu J, Woodard RW. New insights into the evolutionary links relating to the 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase subfamilies. J Biol Chem 2005; 281:4042-8. [PMID: 16339761 DOI: 10.1074/jbc.m512223200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial 3-deoxy-d-arabino-heptulosonate 7-phosphate synthases (DAHPSs) have been divided into either of two classes (Class I/Class II) or subfamilies (AroAI(alpha)/AroAI(beta)). Our investigation into the biochemical properties of the unique bifunctional DAHPS from Bacillus subtilis provides new insight into the evolutionary link among DAHPS subfamilies. In the present study, the DAHPS (aroA) and chorismate mutase (aroQ) activities of B. subtilis DAHPS are separated by domain truncation. Detailed enzymatic studies with the full-length wild-type protein and the truncated domains led to our hypothesis that the aroQ domain was fused to the N terminus of aroA in B. subtilis during evolution for the purpose of feedback regulation and not for the creation of a bona fide bifunctional enzyme. In addition, examination of aroA and aroQ fusion proteins from Porphyromonas gingivalis, in which the aroQ domain is fused to the C terminus of aroA, further supports the hypothesis. These results, along with sequence structure analysis of the DAHPS families suggest that "feedback regulation" may indeed be the evolutionary link between the two classes/subfamilies. It is likely that DAHPSs evolved from a primitive unregulated member of the AroAI(beta) subfamily. During evolution, some members of the AroAI(beta) subfamily remained unregulated, whereas other members acquired an extra domain for feedback regulation. The AroAI(alpha) subfamilies, however, evolved in a more complex manner to acquire insertions/extensions in the (beta/alpha)(8) barrel to function as regulatory elements.
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Affiliation(s)
- Jing Wu
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, 48109-1065, USA
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24
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Webby C, Patchett M, Parker E. Characterization of a recombinant type II 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Helicobacter pylori. Biochem J 2005; 390:223-30. [PMID: 15853768 PMCID: PMC1184578 DOI: 10.1042/bj20050259] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DAH7P (3-Deoxy-D-arabino-heptulosonate 7-phosphate) synthase catalyses the condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) as the first committed step in the biosynthesis of aromatic compounds in plants and micro-organisms. Previous work has identified two families of DAH7P synthases based on sequence similarity and molecular mass, with the majority of the mechanistic and structural studies being carried out on the type I paralogues from Escherichia coli. Whereas a number of organisms possess genes encoding both type I and type II DAH7P synthases, the pathogen Helicobacter pylori has only a single, type II, enzyme. Recombinant DAH7P synthase from H. pylori was partially solubilized by co-expression with chaperonins GroEL/GroES in E. coli, and purified to homogeneity. The enzyme reaction follows an ordered sequential mechanism with the following kinetic parameters: K(m) (PEP), 3 microM; K(m) (E4P), 6 microM; and kcat, 3.3 s(-1). The enzyme reaction involves interaction of the si face of PEP with the re face of E4P. H. pylori DAH7P synthase is not inhibited by phenylalanine, tyrosine, tryptophan or chorismate. EDTA inactivates the enzyme, and activity is restored by a range of bivalent metal ions, including (in order of decreasing effectiveness) Co2+, Mn2+, Ca2+, Mg2+, Cu2+ and Zn2+. Analysis of type II DAH7P synthase sequences reveals several highly conserved motifs, and comparison with the type I enzymes suggests that catalysis by these two enzyme types occurs on a similar active-site scaffold and that the two DAH7P synthase families may indeed be distantly related.
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Affiliation(s)
- Celia J. Webby
- *Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Mark L. Patchett
- †Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
| | - Emily J. Parker
- *Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- To whom correspondence should be sent, at the following address: Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand (email )
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25
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Webby CJ, Baker HM, Lott JS, Baker EN, Parker EJ. The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes. J Mol Biol 2005; 354:927-39. [PMID: 16288916 DOI: 10.1016/j.jmb.2005.09.093] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/28/2005] [Accepted: 09/29/2005] [Indexed: 11/28/2022]
Abstract
The shikimate pathway, responsible for the biosynthesis of aromatic compounds, is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The first step of this pathway is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). The DAH7PSs have been classified into two apparently unrelated types and, whereas structural data have been obtained for the type I DAH7PSs, no structural information is available for their type II counterparts. The type II DAH7PS from M.tuberculosis has been expressed in Escherichia coli, purified, functionally characterized and crystallized. It is found to be metal ion-dependent and subject to feedback inhibition by phenylalanine, tryptophan, tyrosine and chorismate, with a significant synergistic effect when tryptophan is used in combination with phenylalanine. The crystal structure of M.tuberculosis DAH7PS has been determined by single-wavelength anomalous diffraction and refined at 2.3A in complex with substrate phosphoenolpyruvate and Mn(2+). The structure reveals a tightly associated dimer of (beta/alpha)(8) TIM barrels. The monomer fold, the arrangement of key residues in the active site, and the binding modes of PEP and Mn(2+), all match those of the type I enzymes, and indicate a common ancestry for the type I and type II DAH7PSs, despite their minimal sequence identity. In contrast, the structural elements that decorate the core (beta/alpha)(8) fold differ from those in the type I enzymes, consistent with their different regulatory and oligomeric properties.
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Affiliation(s)
- Celia J Webby
- Centre of Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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26
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Ahn M, Pietersma AL, Schofield LR, Parker EJ. Mechanistic divergence of two closely related aldol-like enzyme-catalysed reactions. Org Biomol Chem 2005; 3:4046-9. [PMID: 16267580 DOI: 10.1039/b511661a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The analysis of the interaction of threose 4-phosphate and 2-deoxyerythrose 4-phosphate with 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) reveals previously unrecognised mechanistic differences between the DAH7PS-catalysed reaction and that catalysed by the closely related enzyme, 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS).
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Affiliation(s)
- Meekyung Ahn
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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27
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Rizzi C, Frazzon J, Ely F, Weber PG, da Fonseca IO, Gallas M, Oliveira JS, Mendes MA, de Souza BM, Palma MS, Santos DS, Basso LA. DAHP synthase from Mycobacterium tuberculosis H37Rv: cloning, expression, and purification of functional enzyme. Protein Expr Purif 2005; 40:23-30. [PMID: 15721768 DOI: 10.1016/j.pep.2004.06.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Revised: 06/18/2004] [Indexed: 10/26/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains the leading cause of mortality due to a bacterial pathogen. According to the 2004 Global TB Control Report of the World Health Organization, there are 300,000 new cases per year of multi-drug resistant strains (MDR-TB), defined as resistant to isoniazid and rifampicin, and 79% of MDR-TB cases are now "super strains," resistant to at least three of the four main drugs used to treat TB. Thus there is a need for the development of effective new agents to treat TB. The shikimate pathway is an attractive target for the development of antimycobacterial agents because it has been shown to be essential for the viability of M. tuberculosis, but absent from mammals. The M. tuberculosis aroG-encoded 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (mtDAHPS) catalyzes the first committed step in this pathway. Here we describe the PCR amplification, cloning, and sequencing of aroG structural gene from M. tuberculosis H37Rv. The expression of recombinant mtDAHPS protein in the soluble form was obtained in Escherichia coli Rosetta-gami (DE3) host cells without IPTG induction. An approximately threefold purification protocol yielded homogeneous enzyme with a specific activity value of 0.47U mg(-1) under the experimental conditions used. Gel filtration chromatography results demonstrate that recombinant mtDAHPS is a pentamer in solution. The availability of homogeneous mtDAHPS will allow structural and kinetics studies to be performed aiming at antitubercular agents development.
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Affiliation(s)
- Caroline Rizzi
- Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-970, Brazil
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