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Li M, Tadfie H, Darnell CG, Holland CK. Biochemical investigation of the tryptophan biosynthetic enzyme anthranilate phosphoribosyltransferase in plants. J Biol Chem 2023; 299:105197. [PMID: 37659723 PMCID: PMC10520873 DOI: 10.1016/j.jbc.2023.105197] [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: 07/08/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023] Open
Abstract
While mammals require the essential amino acid tryptophan (Trp) in their diet, plants and microorganisms synthesize Trp de novo. The five-step Trp pathway starts with the shikimate pathway product, chorismate. Chorismate is converted to the aromatic compound anthranilate, which is then conjugated to a phosphoribosyl sugar in the second step by anthranilate phosphoribosyltransferase (PAT1). As a single-copy gene in plants, all fixed carbon flux to indole and Trp for protein synthesis, specialized metabolism, and auxin hormone biosynthesis proceeds through PAT1. While bacterial PAT1s have been studied extensively, plant PAT1s have escaped biochemical characterization. Using a structure model, we identified putative active site residues that were variable across plants and kinetically characterized six PAT1s (Arabidopsis thaliana (thale cress), Citrus sinensis (sweet orange), Pistacia vera (pistachio), Juglans regia (English walnut), Selaginella moellendorffii (spike moss), and Physcomitrium patens (spreading earth-moss)). We probed the catalytic efficiency, substrate promiscuity, and regulation of these six enzymes and found that the C. sinensis PAT1 is highly specific for its cognate substrate, anthranilate. Investigations of site-directed mutants of the A. thaliana PAT1 uncovered an active site residue that contributes to promiscuity. While Trp inhibits bacterial PAT1 enzymes, the six plant PAT1s that we tested were not modulated by Trp. Instead, the P. patens PAT1 was inhibited by tyrosine, and the S. moellendorffii PAT1 was inhibited by phenylalanine. This structure-informed biochemical examination identified variations in activity, efficiency, specificity, and enzyme-level regulation across PAT1s from evolutionarily diverse plants.
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Affiliation(s)
- Miriam Li
- Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Hisham Tadfie
- Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Cameron G Darnell
- Department of Biology, Williams College, Williamstown, Massachusetts, USA
| | - Cynthia K Holland
- Department of Biology, Williams College, Williamstown, Massachusetts, USA.
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2
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Naz S, Liu P, Farooq U, Ma H. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microb Cell Fact 2023; 22:161. [PMID: 37612753 PMCID: PMC10464499 DOI: 10.1186/s12934-023-02178-z] [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: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023] Open
Abstract
Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.
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Affiliation(s)
- Sadia Naz
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pi Liu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Islamabad, 22060, Pakistan
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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3
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Liu Y, Wu P, Li B, Wang W, Zhu B. Phosphoribosyltransferases and Their Roles in Plant Development and Abiotic Stress Response. Int J Mol Sci 2023; 24:11828. [PMID: 37511586 PMCID: PMC10380321 DOI: 10.3390/ijms241411828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Glycosylation is a widespread glycosyl modification that regulates gene expression and metabolite bioactivity in all life processes of plants. Phosphoribosylation is a special glycosyl modification catalyzed by phosphoribosyltransferase (PRTase), which functions as a key step in the biosynthesis pathway of purine and pyrimidine nucleotides, histidine, tryptophan, and coenzyme NAD(P)+ to control the production of these essential metabolites. Studies in the past decades have reported that PRTases are indispensable for plant survival and thriving, whereas the complicated physiological role of PRTases in plant life and their crosstalk is not well understood. Here, we comprehensively overview and critically discuss the recent findings on PRTases, including their classification, as well as the function and crosstalk in regulating plant development, abiotic stress response, and the balance of growth and stress responses. This review aims to increase the understanding of the role of plant PRTase and also contribute to future research on the trade-off between plant growth and stress response.
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Affiliation(s)
- Ye Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Peiwen Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Bowen Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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4
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Scully TW, Jiao W, Mittelstädt G, Parker EJ. Structure, mechanism and inhibition of anthranilate phosphoribosyltransferase. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220039. [PMID: 36633281 PMCID: PMC9835598 DOI: 10.1098/rstb.2022.0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Anthranilate phosphoribosyltransferase catalyses the second reaction in the biosynthesis of tryptophan from chorismate in microorganisms and plants. The enzyme is homodimeric with the active site located in the hinge region between two domains. A range of structures in complex with the substrates, substrate analogues and inhibitors have been determined, and these have provided insights into the catalytic mechanism of this enzyme. Substrate 5-phospho-d-ribose 1-diphosphate (PRPP) binds to the C-terminal domain and coordinates to Mg2+, in a site completed by two flexible loops. Binding of the second substrate anthranilate is more complex, featuring multiple binding sites along an anthranilate channel. This multi-modal binding is consistent with the substrate inhibition observed at high concentrations of anthranilate. A series of structures predict a dissociative mechanism for the reaction, similar to the reaction mechanisms elucidated for other phosphoribosyltransferases. As this enzyme is essential for some pathogens, efforts have been made to develop inhibitors for this enzyme. To date, the best inhibitors exploit the multiple binding sites for anthranilate. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Thomas W. Scully
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Gerd Mittelstädt
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Emily J. Parker
- Ferrier Research Institute, Victoria University of Wellington, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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Wu X, Zhang M, Kuang Z, Yue J, Xue L, Zhu M, Zhu Z, Khan MH, Niu L. Crystal structures of anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2021; 77:61-69. [PMID: 33682790 PMCID: PMC7938636 DOI: 10.1107/s2053230x21001989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/19/2021] [Indexed: 11/10/2022] Open
Abstract
Anthranilate phosphoribosyltransferase (AnPRT) catalyzes the transfer of the phosphoribosyl group of 5'-phosphoribosyl-1'-pyrophosphate (PRPP) to anthranilate to form phosphoribosyl-anthranilate. Crystal structures of AnPRTs from bacteria and archaea have previously been determined; however, the structure of Saccharomyces cerevisiae AnPRT (ScAnPRT) still remains unsolved. Here, crystal structures of ScAnPRT in the apo form as well as in complex with its substrate PRPP and the substrate analogue 4-fluoroanthranilate (4FA) are presented. These structures demonstrate that ScAnPRT exhibits the conserved structural fold of type III phosphoribosyltransferase enzymes and shares the similar mode of substrate binding found across the AnPRT protein family. In addition, crystal structures of ScAnPRT mutants (ScAnPRTSer121Ala and ScAnPRTGly141Asn) were also determined. These structures suggested that the conserved residue Ser121 is critical for binding PRPP, while Gly141 is dispensable for binding 4FA. In summary, these structures improved the preliminary understanding of the substrate-binding mode of ScAnPRT and laid foundations for future research.
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Affiliation(s)
- Xiaofei Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Mengying Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Zhiling Kuang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Jian Yue
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Lu Xue
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Min Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Zhongliang Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Muhammad Hidayatullah Khan
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
| | - Liwen Niu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui 230026, People’s Republic of China
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6
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Schlee S, Straub K, Schwab T, Kinateder T, Merkl R, Sterner R. Prediction of quaternary structure by analysis of hot spot residues in protein-protein interfaces: the case of anthranilate phosphoribosyltransferases. Proteins 2019; 87:815-825. [PMID: 31134642 DOI: 10.1002/prot.25744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/06/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022]
Abstract
It is an important goal of computational biology to correctly predict the association state of a protein based on its amino acid sequence and the structures of known homologues. We have pursued this goal on the example of anthranilate phosphoribosyltransferase (AnPRT), an enzyme that is involved in the biosynthesis of the amino acid tryptophan. Firstly, known crystal structures of naturally occurring homodimeric AnPRTs were analyzed using the Protein Interfaces, Surfaces, and Assemblies (PISA) service of the European Bioinformatics Institute (EBI). This led to the identification of two hydrophobic "hot spot" amino acids in the protein-protein interface that were predicted to be essential for self-association. Next, in a comprehensive multiple sequence alignment (MSA), naturally occurring AnPRT variants with hydrophilic or charged amino acids in place of hydrophobic residues in the two hot spot positions were identified. Representative variants were characterized in terms of thermal stability, enzymatic activity, and quaternary structure. We found that AnPRT variants with charged residues in both hot spot positions exist exclusively as monomers in solution. Variants with hydrophilic amino acids in one hot spot position occur in both forms, monomer and dimer. The results of the present study provide a detailed characterization of the determinants of the AnPRT monomer-dimer equilibrium and show that analysis of hot spots in combination with MSAs can be a valuable tool in prediction of protein quaternary structures.
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Affiliation(s)
- Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Schwab
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
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7
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Evans GL, Furkert DP, Abermil N, Kundu P, de Lange KM, Parker EJ, Brimble MA, Baker EN, Lott JS. Datasets, processing and refinement details for Mtb-AnPRT: inhibitor structures with various space groups. Data Brief 2017; 15:1019-1029. [PMID: 29167811 PMCID: PMC5686470 DOI: 10.1016/j.dib.2017.10.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/21/2022] Open
Abstract
There are twenty-five published structures of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (Mtb-AnPRT) that use the same crystallization protocol. The structures include protein complexed with natural and alternative substrates, protein:inhibitor complexes, and variants with mutations of substrate-binding residues. Amongst these are varying space groups (i.e. P21, C2, P21212, P212121). This article outlines experimental details for 3 additional Mtb-AnPRT:inhibitor structures. For one protein:inhibitor complex, two datasets are presented – one generated by crystallization of protein in the presence of the inhibitor and another where a protein crystal was soaked with the inhibitor. Automatic and manual processing of these datasets indicated the same space group for both datasets and thus indicate that the space group differences between structures of Mtb-AnPRT:ligand complexes are not related to the method used to introduce the ligand.
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Affiliation(s)
- Genevieve L Evans
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Daniel P Furkert
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Nacim Abermil
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Preeti Kundu
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Katrina M de Lange
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P.O. Box 4800, Christchurch 8140, New Zealand
| | - Margaret A Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - J Shaun Lott
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
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8
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Evans GL, Furkert DP, Abermil N, Kundu P, de Lange KM, Parker EJ, Brimble MA, Baker EN, Lott JS. Anthranilate phosphoribosyltransferase: Binding determinants for 5'-phospho-alpha-d-ribosyl-1'-pyrophosphate (PRPP) and the implications for inhibitor design. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:264-274. [PMID: 28844746 DOI: 10.1016/j.bbapap.2017.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 07/07/2017] [Accepted: 08/07/2017] [Indexed: 12/17/2022]
Abstract
Phosphoribosyltransferases (PRTs) bind 5'-phospho-α-d-ribosyl-1'-pyrophosphate (PRPP) and transfer its phosphoribosyl group (PRib) to specific nucleophiles. Anthranilate PRT (AnPRT) is a promiscuous PRT that can phosphoribosylate both anthranilate and alternative substrates, and is the only example of a type III PRT. Comparison of the PRPP binding mode in type I, II and III PRTs indicates that AnPRT does not bind PRPP, or nearby metals, in the same conformation as other PRTs. A structure with a stereoisomer of PRPP bound to AnPRT from Mycobacterium tuberculosis (Mtb) suggests a catalytic or post-catalytic state that links PRib movement to metal movement. Crystal structures of Mtb-AnPRT in complex with PRPP and with varying occupancies of the two metal binding sites, complemented by activity assay data, indicate that this type III PRT binds a single metal-coordinated species of PRPP, while an adjacent second metal site can be occupied due to a separate binding event. A series of compounds were synthesized that included a phosphonate group to probe PRPP binding site. Compounds containing a "bianthranilate"-like moiety are inhibitors with IC50 values of 10-60μM, and Ki values of 1.3-15μM. Structures of Mtb-AnPRT in complex with these compounds indicate that their phosphonate moieties are unable to mimic the binding modes of the PRib or pyrophosphate moieties of PRPP. The AnPRT structures presented herein indicated that PRPP binds a surface cleft and becomes enclosed due to re-positioning of two mobile loops.
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Affiliation(s)
- Genevieve L Evans
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand.
| | - Daniel P Furkert
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Nacim Abermil
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Preeti Kundu
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; Biomolecular Interaction Centre, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand; Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Katrina M de Lange
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; Biomolecular Interaction Centre, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand; Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand
| | - Margaret A Brimble
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1142, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - J Shaun Lott
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand; School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand.
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9
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Perveen S, Rashid N, Tang XF, Imanaka T, Papageorgiou AC. Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure. FEBS Open Bio 2017; 7:1217-1230. [PMID: 28781961 PMCID: PMC5537072 DOI: 10.1002/2211-5463.12264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/12/2022] Open
Abstract
Anthranilate phosphoribosyltransferase (TrpD) is involved in tryptophan biosynthesis, catalyzing the transfer of a phosphoribosyl group to anthranilate, leading to the generation of phosphoribosyl anthranilate. TrpD belongs to the phosphoribosyltransferase (PRT) superfamily and is the only member of the structural class IV. X-ray structures of TrpD from seven species have been solved to date. Here, functional and structural characterization of a recombinant TrpD from hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (TkTrpD) was carried out. Contrary to previously characterized Mg2+-dependent TrpD enzymes, TkTrpD was found to have a unique divalent cation dependency characterized by maximum activity in the presence of Zn2+ (1580 μmol·min-1·mg-1, the highest reported for any TrpD) followed by Ca2+ (948 μmol·min-1·mg-1) and Mg2+ (711 μmol·min-1·mg-1). TkTrpD displayed an unusually low thermostability compared to other previously characterized proteins from T. kodakarensis KOD1. The crystal structure of TkTrpD was determined in free form and in the presence of Zn2+ to 1.9 and 2.4 Å resolutions, respectively. TkTrpD structure displayed the typical PRT fold similar to other class IV PRTs, with a small N-terminal α-helical domain and a larger C-terminal α/β domain. Electron densities for Zn2+ were identified at the expected zinc-binding motif, DE(217-218), of the enzyme in each subunit of the dimer. Two additional Zn2+ were found at a new dimer interface formed in the presence of Zn2+. A fifth Zn2+ was found bound to Glu118 at crystal lattice contacts and a sixth one was ligated with Glu235. Based on the TkTrpD-Zn2+ structure, it is suggested that the formation of a new dimer may be responsible for the higher enzyme activity of TkTrpD in the presence of Zn2+ ions.
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Affiliation(s)
- Sumera Perveen
- School of Biological Sciences University of the Punjab Lahore Pakistan.,Turku Centre for Biotechnology University of Turku and Åbo Akademi University Finland
| | - Naeem Rashid
- School of Biological Sciences University of the Punjab Lahore Pakistan
| | - Xiao-Feng Tang
- Department of Microbiology College of Life Sciences Wuhan University Hubei Province China
| | - Tadayuki Imanaka
- The Research Organization of Science and Technology Ritsumeikan University Kusatsu Shiga Japan
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Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. Microbiol Mol Biol Rev 2016; 81:81/1/e00040-16. [PMID: 28031352 DOI: 10.1128/mmbr.00040-16] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.
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11
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Cookson TVM, Evans GL, Castell A, Baker EN, Lott JS, Parker EJ. Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site. Biochemistry 2016; 54:6082-92. [PMID: 26356348 DOI: 10.1021/acs.biochem.5b00612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Anthranilate phosphoribosyltransferase (AnPRT) is essential for the biosynthesis of tryptophan in Mycobacterium tuberculosis (Mtb). This enzyme catalyzes the second committed step in tryptophan biosynthesis, the Mg²⁺-dependent reaction between 5'-phosphoribosyl-1'-pyrophosphate (PRPP) and anthranilate. The roles of residues predicted to be involved in anthranilate binding have been tested by the analysis of six Mtb-AnPRT variant proteins. Kinetic analysis showed that five of six variants were active and identified the conserved residue R193 as being crucial for both anthranilate binding and catalytic function. Crystal structures of these Mtb-AnPRT variants reveal the ability of anthranilate to bind in three sites along an extended anthranilate tunnel and expose the role of the mobile β2-α6 loop in facilitating the enzyme's sequential reaction mechanism. The β2-α6 loop moves sequentially between a "folded" conformation, partially occluding the anthranilate tunnel, via an "open" position to a "closed" conformation, which supports PRPP binding and allows anthranilate access via the tunnel to the active site. The return of the β2-α6 loop to the "folded" conformation completes the catalytic cycle, concordantly allowing the active site to eject the product PRA and rebind anthranilate at the opening of the anthranilate tunnel for subsequent reactions. Multiple anthranilate molecules blocking the anthranilate tunnel prevent the β2-α6 loop from undergoing the conformational changes required for catalysis, thus accounting for the unusual substrate inhibition of this enzyme.
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Affiliation(s)
- Tammie V M Cookson
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, and Department of Chemistry, University of Canterbury , 20 Kirkwood Avenue, Christchurch 8140, New Zealand
| | - Genevieve L Evans
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Alina Castell
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - J Shaun Lott
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, and Department of Chemistry, University of Canterbury , 20 Kirkwood Avenue, Christchurch 8140, New Zealand
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12
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Schneider D, Kaiser W, Stutz C, Holinski A, Mayans O, Babinger P. YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family of Prokaryotic DNA-binding Proteins. J Biol Chem 2015; 290:19527-39. [PMID: 26063803 DOI: 10.1074/jbc.m114.620575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 12/28/2022] Open
Abstract
We present the crystal structure and biochemical characterization of Escherichia coli YbiB, a member of the hitherto uncharacterized TrpD2 protein family. Our results demonstrate that the functional diversity of proteins with a common fold can be far greater than predictable by computational annotation. The TrpD2 proteins show high structural homology to anthranilate phosphoribosyltransferase (TrpD) and nucleoside phosphorylase class II enzymes but bind with high affinity (KD = 10-100 nM) to nucleic acids without detectable sequence specificity. The difference in affinity between single- and double-stranded DNA is minor. Results suggest that multiple YbiB molecules bind to one longer DNA molecule in a cooperative manner. The YbiB protein is a homodimer that, therefore, has two electropositive DNA binding grooves. But due to negative cooperativity within the dimer, only one groove binds DNA in in vitro experiments. A monomerized variant remains able to bind DNA with similar affinity, but the negative cooperative effect is eliminated. The ybiB gene forms an operon with the DNA helicase gene dinG and is under LexA control, being induced by DNA-damaging agents. Thus, speculatively, the TrpD2 proteins may be part of the LexA-controlled SOS response in bacteria.
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Affiliation(s)
- Daniel Schneider
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Wolfgang Kaiser
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Cian Stutz
- the Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland, and
| | - Alexandra Holinski
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Olga Mayans
- the Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland, and the Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Patrick Babinger
- From the Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany,
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13
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Alternative substrates reveal catalytic cycle and key binding events in the reaction catalysed by anthranilate phosphoribosyltransferase from Mycobacterium tuberculosis. Biochem J 2014; 461:87-98. [PMID: 24712732 DOI: 10.1042/bj20140209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AnPRT (anthranilate phosphoribosyltransferase), required for the biosynthesis of tryptophan, is essential for the virulence of Mycobacterium tuberculosis (Mtb). AnPRT catalyses the Mg2+-dependent transfer of a phosphoribosyl group from PRPP (5'-phosphoribosyl-1'-pyrophosphate) to anthranilate to form PRA (5'-phosphoribosyl anthranilate). Mtb-AnPRT was shown to catalyse a sequential reaction and significant substrate inhibition by anthranilate was observed. Antimycobacterial fluoroanthranilates and methyl-substituted analogues were shown to act as alternative substrates for Mtb-AnPRT, producing the corresponding substituted PRA products. Structures of the enzyme complexed with anthranilate analogues reveal two distinct binding sites for anthranilate. One site is located over 8 Å (1 Å=0.1 nm) from PRPP at the entrance to a tunnel leading to the active site, whereas in the second, inner, site anthranilate is adjacent to PRPP, in a catalytically relevant position. Soaking the analogues for variable periods of time provides evidence for anthranilate located at transient positions during transfer from the outer site to the inner catalytic site. PRPP and Mg2+ binding have been shown to be associated with the rearrangement of two flexible loops, which is required to complete the inner anthranilate-binding site. It is proposed that anthranilate first binds to the outer site, providing an unusual mechanism for substrate capture and efficient transfer to the catalytic site following the binding of PRPP.
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14
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Wang H, Godage HY, Riley AM, Weaver JD, Shears SB, Potter BVL. Synthetic inositol phosphate analogs reveal that PPIP5K2 has a surface-mounted substrate capture site that is a target for drug discovery. ACTA ACUST UNITED AC 2014; 21:689-99. [PMID: 24768307 PMCID: PMC4085797 DOI: 10.1016/j.chembiol.2014.03.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/28/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
Diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) is one of the mammalian PPIP5K isoforms responsible for synthesis of diphosphoinositol polyphosphates (inositol pyrophosphates; PP-InsPs), regulatory molecules that function at the interface of cell signaling and organismic homeostasis. The development of drugs that inhibit PPIP5K2 could have both experimental and therapeutic applications. Here, we describe a synthetic strategy for producing naturally occurring 5-PP-InsP4, as well as several inositol polyphosphate analogs, and we study their interactions with PPIP5K2 using biochemical and structural approaches. These experiments uncover an additional ligand-binding site on the surface of PPIP5K2, adjacent to the catalytic pocket. This site facilitates substrate capture from the bulk phase, prior to transfer into the catalytic pocket. In addition to demonstrating a “catch-and-pass” reaction mechanism in a small molecule kinase, we demonstrate that binding of our analogs to the substrate capture site inhibits PPIP5K2. This work suggests that the substrate-binding site offers new opportunities for targeted drug design. Chemical synthesis of 5-PP-InsP4 and a diphosphorylated analog Chemical synthesis of inositol polyphosphate analogs with hydrophobic groups An inositol pyrophosphate kinase has a surface-mounted, substrate capture site Structural and biochemical characterization of a catch-and-pass catalytic cycle
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Affiliation(s)
- Huanchen Wang
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Himali Y Godage
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK
| | - Andrew M Riley
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK
| | - Jeremy D Weaver
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stephen B Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Barry V L Potter
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath, Somerset BA2 7AY, UK.
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15
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Evans GL, Gamage SA, Bulloch EMM, Baker EN, Denny WA, Lott JS. Repurposing the Chemical Scaffold of the Anti-Arthritic Drug Lobenzarit to Target Tryptophan Biosynthesis inMycobacterium tuberculosis. Chembiochem 2014; 15:852-64. [DOI: 10.1002/cbic.201300628] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Indexed: 11/10/2022]
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16
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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: 2.0] [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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17
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Castell A, Short FL, Evans GL, Cookson TVM, Bulloch EMM, Joseph DDA, Lee CE, Parker EJ, Baker EN, Lott JS. The Substrate Capture Mechanism of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Provides a Mode for Inhibition. Biochemistry 2013; 52:1776-87. [DOI: 10.1021/bi301387m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alina Castell
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Francesca L. Short
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Genevieve L. Evans
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Tammie V. M. Cookson
- Maurice Wilkins Centre for Molecular
Biodiscovery and Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8140,
New Zealand
| | - Esther M. M. Bulloch
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Dmitri D. A. Joseph
- Maurice Wilkins Centre for Molecular
Biodiscovery and Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8140,
New Zealand
| | - Clare E. Lee
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J. Parker
- Maurice Wilkins Centre for Molecular
Biodiscovery and Department of Chemistry, University of Canterbury, 20 Kirkwood Avenue, Christchurch 8140,
New Zealand
| | - Edward N. Baker
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
| | - J. Shaun Lott
- Maurice Wilkins
Centre for Molecular
Biodiscovery and School of Biological Sciences, University of Auckland, 3 Symonds Street, Auckland 1142, New Zealand
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18
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Lambrecht JA, Downs DM. Anthranilate phosphoribosyl transferase (TrpD) generates phosphoribosylamine for thiamine synthesis from enamines and phosphoribosyl pyrophosphate. ACS Chem Biol 2013; 8:242-8. [PMID: 23101964 DOI: 10.1021/cb300364k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anthranilate phosphoribosyl transferase (TrpD) has been well characterized for its role in the tryptophan biosynthetic pathway. Here, we characterized a new reaction catalyzed by TrpD that resulted in the formation of the purine/thiamine intermediate metabolite phosphoribosylamine (PRA). The data showed that 4- and 5-carbon enamines served as substrates for TrpD, and the reaction product was predicted to be a phosphoribosyl-enamine adduct. Isotopic labeling data indicated that the TrpD reaction product was hydrolyzed to PRA. Variants of TrpD that were proficient for tryptophan synthesis were unable to support PRA formation in vivo in Salmonella enterica. These protein variants had substitutions at residues that contributed to binding substrates anthranilate or phosphoribosyl pyrophosphate (PRPP). Taken together the data herein identified a new reaction catalyzed by a well-characterized biosynthetic enzyme, and both illustrated the robustness of the metabolic network and identified a role for an enamine that accumulates in the absence of reactive intermediate deaminase RidA.
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Affiliation(s)
- Jennifer A. Lambrecht
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United
States
| | - Diana M. Downs
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United
States
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19
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Dietrich S, Borst N, Schlee S, Schneider D, Janda JO, Sterner R, Merkl R. Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple-sequence alignments. Biochemistry 2012; 51:5633-41. [PMID: 22737967 DOI: 10.1021/bi300747r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The analysis of a multiple-sequence alignment (MSA) with correlation methods identifies pairs of residue positions whose occupation with amino acids changes in a concerted manner. It is plausible to assume that positions that are part of many such correlation pairs are important for protein function or stability. We have used the algorithm H2r to identify positions k in the MSAs of the enzymes anthranilate phosphoribosyl transferase (AnPRT) and indole-3-glycerol phosphate synthase (IGPS) that show a high conn(k) value, i.e., a large number of significant correlations in which k is involved. The importance of the identified residues was experimentally validated by performing mutagenesis studies with sAnPRT and sIGPS from the archaeon Sulfolobus solfataricus. For sAnPRT, five H2r mutant proteins were generated by replacing nonconserved residues with alanine or the prevalent residue of the MSA. As a control, five residues with conn(k) values of zero were chosen randomly and replaced with alanine. The catalytic activities and conformational stabilities of the H2r and control mutant proteins were analyzed by steady-state enzyme kinetics and thermal unfolding studies. Compared to wild-type sAnPRT, the catalytic efficiencies (k(cat)/K(M)) were largely unaltered. In contrast, the apparent thermal unfolding temperature (T(M)(app)) was lowered in most proteins. Remarkably, the strongest observed destabilization (ΔT(M)(app) = 14 °C) was caused by the V284A exchange, which pertains to the position with the highest correlation signal [conn(k) = 11]. For sIGPS, six H2r mutant and four control proteins with alanine exchanges were generated and characterized. The k(cat)/K(M) values of four H2r mutant proteins were reduced between 13- and 120-fold, and their T(M)(app) values were decreased by up to 5 °C. For the sIGPS control proteins, the observed activity and stability decreases were much less severe. Our findings demonstrate that positions with high conn(k) values have an increased probability of being important for enzyme function or stability.
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Affiliation(s)
- Susanne Dietrich
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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20
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Schwab T, Sterner R. Stabilization of a metabolic enzyme by library selection in Thermus thermophilus. Chembiochem 2011; 12:1581-8. [PMID: 21455924 DOI: 10.1002/cbic.201000770] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Indexed: 11/11/2022]
Abstract
The anthranilate phosphoribosyl transferase from the hyperthermophilic archaeon Sulfolobus solfataricus (sAnPRT, encoded by strpD), which catalyzes the third step in tryptophan biosynthesis, is a thermostable homodimer with low enzymatic activity at room temperature. We have combined two mutations leading to the monomerization and two mutations leading to the activation of sAnPRT. The resulting "activated monomer" sAnPRT-I36E-M47D+D83G-F149S, which is much more labile than wild-type sAnPRT, was stabilized by a combination of random mutagenesis and metabolic library selection using the extremely thermophilic bacterium Thermus thermophilus as host. This approach led to the identification of five mutations that individually increased the thermal stability of sAnPRT-I36E-M47D+D83G-F149S by 1 to 8 °C, and by 13 °C when combined. The beneficial exchanges were located in different parts of the protein structure, but none of them led to the "re-dimerization" of the enzyme. We observed a negative correlation between thermal stability and catalytic activity of the mutants; this suggests that conformational flexibility is required for catalysis by sAnPRT.
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Affiliation(s)
- Thomas Schwab
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
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21
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Schlee S, Deuss M, Bruning M, Ivens A, Schwab T, Hellmann N, Mayans O, Sterner R. Activation of anthranilate phosphoribosyltransferase from Sulfolobus solfataricus by removal of magnesium inhibition and acceleration of product release . Biochemistry 2009; 48:5199-209. [PMID: 19385665 DOI: 10.1021/bi802335s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Sulfolobus solfataricus (ssAnPRT) is encoded by the sstrpD gene and catalyzes the reaction of anthranilate (AA) with a complex of Mg(2+) and 5'-phosphoribosyl-alpha1-pyrophosphate (Mg.PRPP) to N-(5'-phosphoribosyl)-anthranilate (PRA) and pyrophosphate (PP(i)) within tryptophan biosynthesis. The ssAnPRT enzyme is highly thermostable (half-life at 85 degrees C = 35 min) but only marginally active at ambient temperatures (turnover number at 37 degrees C = 0.33 s(-1)). To understand the reason for the poor catalytic proficiency of ssAnPRT, we have isolated from an sstrpD library the activated ssAnPRT-D83G + F149S double mutant by metabolic complementation of an auxotrophic Escherichia coli strain. Whereas the activity of purified wild-type ssAnPRT is strongly reduced in the presence of high concentrations of Mg(2+) ions, this inhibition is no longer observed in the double mutant and the ssAnPRT-D83G single mutant. The comparison of the crystal structures of activated and wild-type ssAnPRT shows that the D83G mutation alters the binding mode of the substrate Mg.PRPP. Analysis of PRPP and Mg(2+)-dependent enzymatic activity indicates that this leads to a decreased affinity for a second Mg(2+) ion and thus reduces the concentration of enzymes with the inhibitory Mg(2).PRPP complex bound to the active site. Moreover, the turnover number of the double mutant ssAnPRT-D83G + F149S is elevated 40-fold compared to the wild-type enzyme, which can be attributed to an accelerated release of the product PRA. This effect appears to be mainly caused by an increased conformational flexibility induced by the F149S mutation, a hypothesis which is supported by the reduced thermal stability of the ssAnPRT-F149S single mutant.
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Affiliation(s)
- Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
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22
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Schwab T, Skegro D, Mayans O, Sterner R. A Rationally Designed Monomeric Variant of Anthranilate Phosphoribosyltransferase from Sulfolobus solfataricus is as Active as the Dimeric Wild-type Enzyme but Less Thermostable. J Mol Biol 2008; 376:506-16. [DOI: 10.1016/j.jmb.2007.11.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 11/14/2007] [Accepted: 11/23/2007] [Indexed: 11/28/2022]
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23
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Koch MHJ, Bras W. Synchrotron radiation studies of non-crystalline systems. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b703892p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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